U.S. patent application number 10/124767 was filed with the patent office on 2003-01-09 for apoa1-interacting proteins and use thereof.
This patent application is currently assigned to Myriad Genetics, Incorporated. Invention is credited to Bartel, Paul, Sugiyama, Janice, Szankasi, Philippe.
Application Number | 20030008373 10/124767 |
Document ID | / |
Family ID | 27383156 |
Filed Date | 2003-01-09 |
United States Patent
Application |
20030008373 |
Kind Code |
A1 |
Bartel, Paul ; et
al. |
January 9, 2003 |
APOA1-interacting proteins and use thereof
Abstract
Protein complexes are provided comprising APOA1 and one or more
APOA1-interacting proteins. The protein complexes are useful in
screening assays for identifying compounds effective in modulating
the protein complexes and in treating and/or preventing diseases
and disorders associated with APOA1 and its interacting partners.
In addition, methods of detecting the protein complexes and
modulating the functions and activities of the protein complexes or
interacting members thereof are also provided.
Inventors: |
Bartel, Paul; (Salt Lake
City, UT) ; Szankasi, Philippe; (Salt Lake City,
UT) ; Sugiyama, Janice; (Salt Lake City, UT) |
Correspondence
Address: |
MYRIAD GENETICS INC.
LEGAL DEPARTMENT
320 WAKARA WAY
SALT LAKE CITY
UT
84108
US
|
Assignee: |
Myriad Genetics,
Incorporated
Salt Lake City
UT
|
Family ID: |
27383156 |
Appl. No.: |
10/124767 |
Filed: |
April 17, 2002 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
|
|
60284220 |
Apr 17, 2001 |
|
|
|
60354899 |
Feb 6, 2002 |
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Current U.S.
Class: |
435/226 ;
435/183; 435/7.1 |
Current CPC
Class: |
G01N 33/566 20130101;
C07K 14/775 20130101; G01N 2500/02 20130101 |
Class at
Publication: |
435/226 ;
435/183; 435/7.1 |
International
Class: |
G01N 033/53; C12N
009/00; C12N 009/64 |
Claims
What is claimed is:
1. An isolated protein complex having a first protein which is
APOA1 or a homologue or derivative or fragment thereof interacting
with a second protein which is a protein selected from the group
consisting of PRA1, GOLGIN-84, Syntaxin 2, APOB and FLJ20724 or a
homologue or derivative or fragment thereof.
2. The isolated protein complex of claim 1, wherein said first
protein is APOA1 and said second protein is a protein selected from
the group consisting of PRA1, GOLGIN-84, Syntaxin 2, APOB and
FLJ20724.
3. The isolated protein complex of claim 1, wherein said first
protein is a first fusion protein containing APOA1 or an APOA1
homologue or fragment.
4. The isolated protein complex of claim 1, wherein said second
protein is a second fusion protein containing a protein selected
from the group consisting of PRA1, GOLGIN-84, Syntaxin 2, APOB and
FLJ20724 or a homologue or fragment thereof.
5. An isolated protein complex comprising a first protein
interacting with a second protein, wherein: (a) said first protein
is selected from the group consisting of (i) APOA1, (ii) an APOA1
fragment capable of interacting with a protein selected from the
group consisting of PRA1, GOLGIN-84, Syntaxin 2, APOB and FLJ20724,
and (iii) a fusion protein containing APOA1 or said APOA1 fragment;
and (b) said second protein is selected from the group consisting
of (1) a protein selected from the group consisting of PRA1,
GOLGIN-84, Syntaxin 2, APOB and FLJ20724, (2) a fragment of a
protein selected from the group consisting of PRA1, GOLGIN-84,
Syntaxin 2, APOB and FLJ20724 and capable of interacting with
APOA1, and (3) a fusion protein containing a protein selected from
the group consisting of PRA1, GOLGIN-84, Syntaxin 2, APOB and
FLJ20724 or said fragment.
6. A protein microarray comprising the protein complex according to
claim 5.
7. A fusion protein having a first polypeptide covalently linked to
a second polypeptide, wherein said first polypeptide is APOA1 or a
homologue or fragment thereof, and wherein said second polypeptide
is a protein selected from the group consisting of PRA1, GOLGIN-84,
Syntaxin 2, APOB and FLJ20724 or a homologue or fragment
thereof.
8. A nucleic acid encoding the fusion protein of claim 7.
9. A method for selecting modulators of the protein complex of
claim 5, comprising: providing the protein complex; contacting said
protein complex with a test compound; and detecting the binding of
said test compound to said protein complex.
10. The method of claim 9, further comprising a step of generating
a data set defining one or more selected test compounds, said data
set being embodied in a transmittable form.
11. A method for selecting modulators of an interaction between a
first protein and a second protein, (a) said first protein being
selected from the group consisting of (i) APOA1, (ii) an APOA1
homologue having an amino acid sequence at least 90% identical to
that of APOA1 and capable of interacting with a protein selected
from the group consisting of PRA1, GOLGIN-84, Syntaxin 2, APOB and
FLJ20724, (iii) an APOA1 fragment capable of interacting with a
protein selected from the group consisting of PRA1, GOLGIN-84,
Syntaxin 2, APOB and FLJ20724, and (iv) a fusion protein containing
APOA1, said APOA1 homologue or said APOA1 fragment; and (b) said
second protein being selected from the group consisting of (1)
PRA1, GOLGIN-84, Syntaxin 2, APOB and FLJ20724, (2) a homologue of
a protein selected from the group consisting of PRA1, GOLGIN-84,
Syntaxin 2, APOB and FLJ20724 having an amino acid sequence at
least 90% identical to. that of said protein and capable of
interacting with APOA1, (3) a fragment of a protein selected from
the group consisting of PRA1, GOLGIN-84, Syntaxin 2, APOB and
FLJ20724 and capable of interacting with APOA1, and (4) a fusion
protein containing a protein selected from the group consisting of
PRA1, GOLGIN-84, Syntaxin 2, APOB and FLJ20724, said protein
homologue or said protein fragment, said method comprising:
contacting said first protein with said second protein in the
presence of a test compound; and detecting the interaction between
said first protein and said second protein.
12. The method of claim 11, wherein at least one of said first and
second proteins is a fusion protein having a detectable tag.
13. The method of claim 11, wherein said contacting step is
conducted in a substantially cell free environment.
14. The method of claim 11, wherein the interaction between said
first protein and said second protein is determined in a host
cell.
15. The method of claim 14, wherein said host cell is a yeast
cell.
16. The method of claim 11, wherein said determining step comprises
measuring the amount of the protein complex formed by said first
and second proteins.
17. The method of claim 11, further comprising a step of generating
a data set defining one or more selected test compounds, said data
set being embodied in a transmittable form.
18. A method for selecting modulators of the protein complex of
claim 5, comprising: contacting said protein complex with a test
compound; and detecting the interaction between said first protein
and said second protein.
19. The method of claim 18, further comprising a step of generating
a data set defining one or more selected test compounds, said data
set being embodied in a transmittable form.
20. A method for selecting modulators of an interaction between a
first polypeptide and a second polypeptide, said first polypeptide
being APOA1 or a homologue or fragment thereof and said second
polypeptide being a protein selected from the group consisting of
PRA1, GOLGIN-84, Syntaxin 2, APOB and FLJ20724 or a homologue or
fragment thereof, said method comprising: providing in a host cell
a first fusion protein having said first polypeptide, and a second
fusion protein having said second polypeptide, wherein a DNA
binding domain is fused to one of said first and second
polypeptides while a transcription-activating domain is fused to
the other of said first and second polypeptides; providing in said
host cell a reporter gene, wherein the transcription of the
reporter gene is controlled by the interaction between the first
polypeptide and the second polypeptide; allowing said first and
second fusion proteins to interact with each other within said host
cell in the presence of a test compound; and determining the
expression of said reporter gene.
21. The method of claim 20, wherein said host cell is a yeast
cell.
22. A method for selecting compounds capable of interfering with
the interaction between a first protein and a second protein,
wherein (a) said first protein is selected from the group
consisting of (i) APOA1, (ii) an APOA1 homologue having an amino
acid sequence at least 90% identical to that of APOA1 and capable
of interacting with a protein selected from the group consisting of
PRA1, GOLGIN-84, Syntaxin 2, APOB and FLJ20724, (iii) an APOA1
fragment capable of interacting with a protein selected from the
group consisting of PRA1, GOLGIN-84, Syntaxin 2, APOB and FLJ20724,
and (iv) a fusion protein containing APOA1, said APOA1 homologue or
said APOA1 fragment; and (b) said second protein is selected from
the group consisting of (1) PRA1, GOLGIN-84, Syntaxin 2, APOB and
FLJ20724, (2) a homologue of a protein selected from the group
consisting of PRA1, GOLGIN-84, Syntaxin 2, APOB and FLJ20724 having
an amino acid sequence at least 90% identical to that of said
protein and capable of interacting with APOA1, (3) a fragment of a
protein selected from the group consisting of PRA1, GOLGIN-84,
Syntaxin 2, APOB and FLJ20724 capable of interacting with APOA1,
and (4) a fusion protein containing a protein selected from the
group consisting of PRA1, GOLGIN-84, Syntaxin 2, APOB and FLJ20724,
said protein homologue or said protein fragment, said method
comprising: contacting said first protein with said second protein
in the presence of a test compound and detecting the interaction
between said first protein and said second protein; and contacting
said first protein with said second protein in the absence of said
test compound and detecting the interaction between said first
protein and said second protein.
23. The method of claim 22, wherein said contacting steps are
conducted in a substantially cell free environment.
24. The method of claim 22, wherein said contacting steps are
conducted in a host cell.
25. The method of claim 22, wherein the first protein is a fusion
protein containing APOA1 or said APOA1 fragment, and said second
protein is a fusion protein containing a protein selected from the
group consisting of PRA1, GOLGIN-84, Syntaxin 2, APOB and FLJ20724
or said protein fragment.
26. The method of claim 22, further comprising a step of generating
a data set defining one or more selected test compounds, said data
set being embodied in a transmittable form.
27. A composition comprising: a first expression vector having a
nucleic acid encoding a first protein; and a second expression
vector having a nucleic acid encoding a second protein, wherein:
(a) said first protein is selected from the group consisting of (i)
APOA1, (ii) an APOA1 homologue having an amino acid sequence at
least 90% identical to that of APOA1 and capable of interacting
with a protein selected from the group consisting of PRA1,
GOLGIN-84, Syntaxin 2, APOB and FLJ20724, (iii) an APOA1 fragment
capable of interacting with a protein selected from the group
consisting of PRA1, GOLGIN-84, Syntaxin 2, APOB and FLJ20724, and
(iv) a fusion protein containing APOA1, said APOA1 homologue or
said APOA1 fragment; and (b) said second protein is selected from
the group consisting of (1) PRA1, GOLGIN-84, Syntaxin 2, APOB and
FLJ20724, (2) a homologue of a protein selected from the group
consisting of PRA1, GOLGIN-84, Syntaxin 2, APOB and FLJ20724 having
an amino acid sequence at least 90% identical to that of said
protein and capable of interacting with APOA1, (3) a fragment of a
protein selected from the group consisting of PRA1, GOLGIN-84,
Syntaxin 2, APOB and FLJ20724 capable of interacting with APOA1,
and (4) a fusion protein containing a protein selected from the
group consisting of PRA1, GOLGIN-84, Syntaxin 2, APOB and FLJ20724,
said protein homologue or said protein fragment.
28. An expression vector comprising: (a) a first nucleic acid
encoding a first protein selected from the group consisting of (i)
APOA1, (ii) an APOA1 homologue having an amino acid sequence at
least 90% identical to that of APOA1 and capable of interacting
with a protein selected from the group consisting of PRA1,
GOLGIN-84, Syntaxin 2, APOB and FLJ20724, (iii) an APOA1 fragment
capable of interacting with a protein selected from the group
consisting of PRA1, GOLGIN-84, Syntaxin 2, APOB and FLJ20724, and
(iv) a fusion protein containing APOA1, said APOA1 homologue or
said APOA1 fragment; and (b) a second nucleic acid encoding a
second protein selected from the group consisting of (1) PRA1,
GOLGIN-84, Syntaxin 2, APOB and FLJ20724, (2) a homologue of a
protein selected from the group consisting of PRA1, GOLGIN-84,
Syntaxin 2, APOB and FLJ20724 having an amino acid sequence at
least 90% identical to that of said protein and capable of
interacting with APOA1, (3) a fragment of a protein selected from
the group consisting of PRA1, GOLGIN-84, Syntaxin 2, APOB and
FLJ20724 and capable of interacting with APOA1, and (4) a fusion
protein containing a protein selected from the group consisting of
PRA1, GOLGIN-84, Syntaxin 2, APOB and FLJ20724, said protein
homologue or said protein fragment.
29. A host cell comprising the expression vector of claim 28.
30. A host cell comprising: a first chimeric expression cassette
having a nucleic acid encoding a first protein; and a second
chimeric expression cassette having a nucleic acid encoding a
second protein, wherein: (a) said first protein is selected from
the group consisting of (i) APOA1, (ii) an APOA1 homologue having
an amino acid sequence at least 90% identical to that of APOA1 and
capable of interacting with a protein selected from the group
consisting of PRA1, GOLGIN-84, Syntaxin 2, APOB and FLJ20724, (iii)
an APOA1 fragment capable of interacting with a protein selected
from the group consisting of PRA1, GOLGIN-84, Syntaxin 2, APOB and
FLJ20724, and (iv) a fusion protein containing APOA1, said APOA1
homologue or said APOA1 fragment; and (b) said second protein is
selected from the group consisting of (1) PRA1, GOLGIN-84, Syntaxin
2, APOB and FLJ20724, (2) a homologue of a protein selected from
the group consisting of PRA1, GOLGIN-84, Syntaxin 2, APOB and
FLJ20724 and having an amino acid sequence at least 90% identical
to that of said protein and capable of interacting with APOA1, (3)
a fragment of a protein selected from the group consisting of PRA1,
GOLGIN-84, Syntaxin 2, APOB and FLJ20724 and capable of interacting
with APOA1, and (4) a fusion protein containing a protein selected
from the group consisting of PRA1, GOLGIN-84, Syntaxin 2, APOB and
FLJ20724, said protein homologue or said protein fragment.
31. The host cell of claim 30, wherein said host cell is a yeast
cell.
32. The host cell of claim 30, wherein said first and second
proteins are fusion proteins.
33. The host cell of claim 30, wherein one of said first and second
nucleic acids is linked to a nucleic acid encoding a DNA binding
domain, and the other of said first and second nucleic acids is
linked to a nucleic acid encoding a transcription-activation
domain, whereby two fusion proteins can be produced in said host
cell.
34. The host cell of claim 30, further comprising a reporter gene,
wherein the expression of the reporter gene is controlled by the
interaction between the first protein and the second protein.
35. A method for providing modulators of a protein-protein
interaction comprising: providing atomic coordinates defining a
three-dimensional structure of the protein complex of claim 5; and
designing or selecting compounds capable of modulating the
interaction between the first and second proteins based on said
atomic coordinates.
36. The method of claim 35, further comprising a step of generating
a data set defining one or more selected test compounds, said data
set being embodied in a transmittable form.
37. A method for providing antagonists of a protein-protein
interaction, comprising: providing atomic coordinates defining a
three-dimensional structure of the protein complex of claim 5; and
designing or selecting compounds capable of interfering with the
interaction between the first and second proteins based on said
atomic coordinates.
38. An isolated antibody selectively immunoreactive with the
protein complex of claim 5.
Description
RELATED U.S. APPLICATIONS
[0001] This application claims priority under 35 U.S.C.
.sctn.119(e) to U.S. Provisional Application Serial No. 60/284,220
filed on Apr. 17, 2001 and U.S. Provisional Application Serial No.
60/354,899 filed on Feb. 6, 2002, both of which are incorporated
herein by reference in their entirety.
FIELD OF THE INVENTION
[0002] The present invention generally relates to protein-protein
interactions, particularly to protein complexes formed by
protein-protein interactions and methods of use thereof.
BACKGROUND OF THE INVENTION
[0003] The prolific output from numerous genomic sequencing
efforts, including the Human Genome Project, is creating an
ever-expanding foundation for large-scale study of protein
function. Indeed, this emerging field of proteomics can
appropriately be viewed as a bridge that connects DNA sequence
information to the physiology and pathology of intact organisms. As
such, proteomics--the large-scale study of protein function--will
likely be starting point for the development of many future
pharmaceuticals. The efficiency of drug development will therefore
depend on the diversity and robustness of the methods used to
elucidate protein function, i.e., the proteomic tools that are
available.
[0004] Several approaches are generally known in the art for
studying protein function. One method is to analyze the DNA
sequence of a particular gene and the amino acid sequence coded by
the gene in the context of sequences of genes with known functions.
Generally, similar functions can be predicted based on sequence
homologies. This "homology method" has been widely used, and
powerful computer programs have been designed to facilitate
homology analysis. See, e.g., Altschul et al., Nucleic Acids Res.,
25:3389-3402 (1997). However, this method is useful only when the
function of a homologous protein is known.
[0005] Another useful approach is to interfere with the expression
of a particular gene in a cell or organism and examine the
consequent phenotypic effects. For example, Fire et al., Nature,
391:806-811 (1998) disclose an "RNA interference" assay in which
double-stranded RNA transcripts corresponding to a particular
target gene are injected into cells or organisms to determine the
phenotype associated with the disrupted expression of that gene.
Alternatively, transgenic technologies can be utilized to delete or
"knock out" a particular gene in an organism and the effect of the
gene knockout is determined. See e.g., Winzeler et al., Science,
285:901-906 (1999); Zambrowicz et al., Nature, 392:608-611 (1998).
The phenotypic effects resulting from the disruption of expression
of a particular gene can shed some light on the functions of the
gene. However, the techniques involved are complex and the time
required for a phenotype to appear can be long, especially in
mammals. In addition, in many cases disruption of a particular gene
may not cause any detectable phenotypic effect.
[0006] Gene functions can also be uncovered by genetic linkage
analysis. For example, genes responsible for certain diseases may
be identified by positional cloning. Alternatively, gene function
may be inferred by comparing genetic variations among individuals
in a population and correlating particular phenotypes with the
genetic variations. Such linkage analyses are powerful tools,
particularly when genetic variations exist in a traceable
population from which samples are readily obtainable. However,
readily identifiable genetic diseases are rare and samples from a
large population with genetic variations are not easily accessible.
In addition, it is also possible that a gene identified in a
linkage analysis does not contribute to the associated disease or
symptom but rather is simply linked to unknown genetic variations
that cause the phenotypic defects.
[0007] With the advance of bioinformatics and publication of the
full genome sequence of many organisms, computational methods have
also been developed to assign protein functions by comparative
genome analysis. For example, Pellegrini et al., Proc. Natl. Acad.
Sci. USA 96:4285-4288 (1999) discloses a method that constructs a
"phylogenetic profile" that summarizes the presence or absence of a
particular protein across a number of organisms as determined by
analyzing the genome sequences of the organisms. A protein's
function is predicted to be linked to another protein's function if
the two proteins share the same phylogenetic profile. Another
method, the Rosetta Stone method, is based on the theory that
separate proteins in one organism are often expressed as separate
domains of a fusion protein in another organism. Because the
separate domains in the fusion protein are predictably associated
with the same function, it can be reasonably predicted that the
separate proteins are associated with same functions. Therefore, by
discovering separate proteins corresponding to a fusion protein,
i.e., the "Rosetta Stone sequence," functional linkage between
proteins can be established. See Marcotte et al., Science,
285:751-753 (1999); Enright et al., Nature, 402:86-90 (1999).
Another computational method is the "gene neighbor method." See
Dandekar et al., Trends Biochem. Sci., 23:324-328 (1998); Overbeek
et al., Proc. Natl. Acad. Sci. USA 96:2896-2901 (1999). This method
is based on the likelihood that if two genes are found to be
neighbors in several different genomes, the proteins encoded by the
genes share a common function.
[0008] While the methods described above are useful in analyzing
protein functions, they are constrained by various practical
limitations such as unavailability of suitable samples, inefficient
assay procedures, and limited reliability. The computational
methods are useful in linking proteins by function. However, they
are only applicable to certain proteins, and the linkage maps
established therewith are sketchy. That is, the maps lack specific
information that describes how proteins function in relation to
each other within the functional network. Indeed, none of the
methods places the identified protein functions in the context of
protein-protein interactions.
[0009] In contrast with the traditional view of protein function,
which focuses on the action of a single protein molecule, a modem
expanded view of protein function defines a protein as an element
in an interaction network. See Eisenberg et al., Nature,
405:823-826 (2000). That is, a full understanding of the functions
of a protein will require knowledge of not only the characteristics
of the protein itself, but also its interactions or connections
with other proteins in the same interacting network. In essence,
protein-protein interactions form the basis of almost all
biological processes, and each biological process is composed of a
network of interacting proteins. For example, cellular structures
such as cytoskeletons, nuclear pores, centrosomes, and kinetochores
are formed by complex interactions among a multitude of proteins.
Many enzymatic reactions are associated with large protein
complexes formed by interactions among enzymes, protein substrates,
and protein modulators. In addition, protein-protein interactions
are also part of the mechanisms for signal transduction and other
basic cellular functions such as DNA replication, transcription,
and translation. For example, the complex transcription initiation
process generally requires protein-protein interactions among
numerous transcription factors, RNA polymerase, and other proteins.
See e.g., Tjian and Maniatis, Cell, 77:5-8 (1994).
[0010] Because most proteins function through their interactions
with other proteins, if a test protein interacts with a known
protein, one can reasonably predict that the test protein is
associated with the functions of the known protein, e.g., in the
same cellular structure or same cellular process as the known
protein. Thus, interaction partners can provide an immediate and
reliable understanding towards the functions of the interacting
proteins. By identifying interacting proteins, a better
understanding of disease pathways and the cellular processes that
result in diseases may be achieved, and important regulators and
potential drug targets in disease pathways can be identified.
[0011] There has been much interest in protein-protein interactions
in the field of proteomics. A number of biochemical approaches have
been used to identify interacting proteins. These approaches
generally employ the affinities between interacting proteins to
isolate proteins in a bound state. Examples of such methods include
coimmunoprecipitation and copurification, optionally combined with
cross-linking to stabilize the binding. Identities of the isolated
protein interacting partners can be characterized by, e.g., mass
spectrometry. See e.g., Rout et al., J. Cell. Biol., 148:635-651
(2000); Houry et al., Nature, 402:147-154 (1999); Winter et al.,
Curr. Biol., 7:517-529 (1997). A popular approach useful in
large-scale screening is the phage display method, in which
filamentous bacteriophage particles are made by recombinant DNA
technologies to express a peptide or protein of interest fused to a
capsid or coat protein of the bacteriophage. A whole library of
peptides or proteins of interest can be expressed and a bait
protein can be used to screening the library to identify peptides
or proteins capable of binding to the bait protein. See e.g., U.S.
Pat. Nos. 5,223,409; 5,403,484; 5,571,698; and 5,837,500. Notably,
the phage display method only identifies those proteins capable of
interacting in an in vitro environment, while the
coimmunoprecipitation and copurification methods are not amenable
to high throughput screening.
[0012] The yeast two-hybrid system is a genetic method that
overcomes certain shortcomings of the above approaches. The yeast
two-hybrid system has proven to be a powerful method for the
discovery of specific protein interactions in vivo. See generally,
Bartel and Fields, eds., The Yeast Two-Hybrid System, Oxford
University Press, New York, N.Y., 1997. The yeast two-hybrid
technique is based on the fact that the DNA-binding domain and the
transcriptional activation domain of a transcriptional activator
contained in different fusion proteins can still activate gene
transcription when they are brought into proximity to each other.
In a yeast two-hybrid system, two fusion proteins are expressed in
yeast cells. One has a DNA-binding domain of a transcriptional
activator fused to a test protein. The other, on the other hand,
includes a transcriptional activating domain of the transcriptional
activator fused to another test protein. If the two test proteins
interact with each other in vivo, the two domains of the
transcriptional activator are brought together reconstituting the
transcriptional activator and activating a reporter gene controlled
by the transcriptional activator. See, e.g., U.S. Pat. No.
5,283,173.
[0013] Because of its simplicity, efficiency and reliability, the
yeast two-hybrid system has gained tremendous popularity in many
areas of research. In addition, yeast cells are eukaryotic cells.
The interactions between mammalian proteins detected in the yeast
two-hybrid system typically are bona fide interactions that occur
in mammalian cells under physiological conditions. As a matter of
fact, numerous mammalian protein-protein interactions have been
identified using the yeast two-hybrid system. The identified
proteins have contributed significantly to the understanding of
many signal transduction pathways and other biological processes.
For example, the yeast two-hybrid system has been successfully
employed in identifying a large number of novel mammalian cell
cycle regulators that are important in complex cell cycle
regulations. Using known proteins that are important in cell cycle
regulation as baits, other proteins involved in cell cycle control
were identified by virtue of their ability to interact with the
baits. See generally, Hannon et al., in The Yeast Two-Hybrid
System, Bartel and Fields, eds., pages 183-196, Oxford University
Press, New York, N.Y., 1997. Examples of mammalian cell cycle
regulators identified by the yeast two-hybrid system include
CDK4/CDK6 inhibitors (e.g., p16, p15, p18 and p19), Rb family
members (e.g., p130), Rb phosphatase (e.g., PP1-.alpha.2),
Rb-binding transcription factors (e.g., E2F-4 and E2F-5), General
CDK inhibitors (e.g., p21 and p27), CAK cyclin (e.g., cyclin H),
and CDK Thr161 phosphatase (e.g., KAP and CDI1). See id at page
192. "[T]he two-hybrid approach promises to be a useful tool in our
ongoing quest for new pieces of the cell cycle puzzle." See id at
page 193.
[0014] The yeast two-hybrid system can be employed to identify
proteins that interact with a specific known protein involved in a
disease pathway, and thus provide valuable understandings of the
disease mechanism. The identified proteins and the protein-protein
interactions in which they participate are potential targets for
use in identifying new drugs for treating the disease.
SUMMARY OF THE INVENTION
[0015] It has been discovered that Apolipoprotein A-I ("APOA1")
specifically interacts with prenylated Rab acceptor 1 ("PRA1", also
known as RABAC1), golgi autoantigen 84 KD protein ("GOLGIN-84"),
Syntaxin 2, apolipoprotein B-100 ("APOB") and hypothetical protein
FLJ20724 ("FLJ20724"). The specific interactions between these
proteins and APOA1 suggest that APOA1 and the APOA1-interacting
proteins are involved in common biological processes. In addition,
the interactions between such APOA1-interacting proteins and APOA1
lead to the formation of protein complexes both in vitro and in
vivo that contain APOA1 and one or more of the APOA1-interacting
proteins. The protein complexes formed under physiological
conditions can mediate the functions and biological activities of
APOA1 and the APOA1-interacting proteins. For example, they may be
involved in cholesterol transport and lipid metabolism. Thus, the
APOA1-interacting proteins and the protein complexes are potential
drug targets for the development of drugs useful in treating or
preventing diseases and disorders associated with the
APOA1-containing protein complexes or a protein member thereof.
[0016] In accordance with a first aspect of the present invention,
isolated protein complexes are provided comprising APOA1 and one or
more APOA1-interacting proteins selected from the group consisting
of PRA1, GOLGIN-84, Syntaxin 2, APOB and FLJ20724. In addition,
homologues, derivatives, and fragments of APOA1 and of the
APOA1-interacting proteins may also be used in forming protein
complexes. In a specific embodiment, fragments of APOA1 and the
APOA1-interacting proteins containing the protein domains
responsible for the interaction between APOA1 and the
APOA1-interacting proteins are used in forming a protein complex of
the present invention. In another embodiment, an interacting
protein member in the protein complexes of the present invention is
a fusion protein containing APOA1 or a homologue, derivative, or
fragment thereof. A fusion protein containing an APOA1-interacting
protein or a homologue, derivative, or fragment thereof may also be
used in the protein complexes. In yet another embodiment, a protein
complex is provided from a hybrid protein, which comprises APOA1 or
a homologue, derivative, or fragment thereof covalently linked,
directly or through a linker, to one of the APOA1-interacting
proteins or a homologue, derivative, or fragment thereof. In
addition, nucleic acids encoding the hybrid protein are also
provided.
[0017] In yet another aspect, the present invention also provides a
method for making the protein complexes. The method includes the
steps of providing the first protein and the second protein in the
protein complexes of the present invention and contacting said
first protein with said second protein. In addition, the protein
complexes can be prepared by isolation or purification from tissues
and cells or produced by recombinant expression of their protein
members. The protein complexes can be incorporated into a protein
microchip or microarray, which are useful in large-scale high
throughput screening assays involving the protein complexes.
[0018] In accordance with a second aspect of the invention,
antibodies are provided that are immunoreactive with a protein
complex of the present invention. In one embodiment, an antibody is
selectively immunoreactive with a protein complex of the present
invention. In another embodiment, a bifunctional antibody is
provided that has two different antigen binding sites, each being
specific to a different interacting protein member in a protein
complex of the present invention. The antibodies of the present
invention can take various forms including polyclonal antibodies,
monoclonal antibodies, chimeric antibodies, antibody fragments such
as Fv fragments, single-chain Fv fragments (scFv), Fab' fragments,
and F(ab').sub.2 fragments. Preferably, the antibodies are
partially or fully humanized antibodies. The antibodies of the
present invention can be readily prepared using procedures
generally known in the art. For example, recombinant libraries such
as phage display libraries and ribosome display libraries may be
used to screen for antibodies with desirable specificities. In
addition, various mutagenesis techniques such as site-directed
mutagenesis and PCR diversification may be used in combination with
the screening assays.
[0019] The present invention also provides detection methods for
determining whether there is any aberration in a patient with
respect to a protein complex having APOA1 and one or more of the
APOA1-interacting proteins. In one embodiment, the method comprises
detecting an aberrant concentration of the protein complexes of the
present invention. Alternatively, the concentrations of one or more
interacting protein members (at the protein or cDNA or mRNA level)
of a protein complex of the present invention are measured. In
addition, the cellular localization, or tissue or organ
distribution of a protein complex of the present invention is
determined to detect any aberrant localization or distribution of
the protein complex. In another embodiment, mutations in one or
more interacting protein members of a protein complex of the
present invention can be detected. In particular, it is desirable
to determine whether the interacting protein members have any
mutations that will lead to, or are associated with, changes in the
functional activity of the proteins or changes in their binding
affinity to other interacting protein members in forming a protein
complex of the present invention. In yet another embodiment, the
binding constant of the interacting protein members of one or more
protein complexes is determined. A kit may be used for conducting
the detection methods of the present invention. Typically, the kit
contains reagents useful in any of the above-described embodiments
of the detection methods, including, e.g., antibodies specific to a
protein complex of the present invention or interacting members
thereof, and oligonucleotides selectively hybridizable to the cDNAs
or mRNAs encoding one or more interacting protein members of a
protein complex. The detection methods may be useful in diagnosing
a disease or disorder such as dementia such as Alzheimer's disease
and cardiovascular diseases such as coronary heart disease,
atherosclerosis, hypercholesterolemia, Tangier disease and
amyloidosis, staging the disease or disorder, or identifying a
predisposition to the disease or disorder.
[0020] The present invention also provides screening methods for
selecting modulators of a protein complex formed between APOA1 or a
homologue, derivative or fragment thereof and one of the
APOA1-interacting proteins or a homologue, derivative, or fragment
thereof. Screening methods are also provided for selecting
modulators of APOA1 or an APOA1-interacting protein. The compounds
identified in the screening methods of the present invention can be
used in modulating the functions or activities of APOA1, the
APOA1-interacting proteins, or the protein complexes of the present
invention. They may also be effective in modulating the cellular
functions involving APOA1, APOA1-interacting proteins or
APOA1-containing protein complexes, and in preventing or
ameliorating diseases or disorders such as dementia such as
Alzheimer's disease and cardiovascular diseases such as coronary
heart disease, atherosclerosis, hypercholesterolemia, Tangier
disease and amyloidosis.
[0021] Thus, test compounds may be screened in in vitro binding
assays to identify compounds capable of binding a protein complex
of the present invention, or APOA1 or an APOA1-interacting protein
identified in accordance with the present invention or homologues,
derivatives or fragments thereof. The assays may include the steps
of contacting the protein complex with a test compound and
detecting the interaction between the interacting partners. In
addition, in vitro dissociation assays may also be employed to
select compounds capable of dissociating or destabilizing the
protein complexes identified in accordance with the present
invention. For example, the assays may entail (1) contacting the
interacting members of the protein complex with each other in the
presence of a test compound; and (2) detecting the interaction
between the interacting members. An in vitro screening assay may
also be used to identify compounds that trigger or initiate the
formation of, or stabilize, a protein complex of the present
invention.
[0022] In preferred embodiments, in vivo assays such as yeast
two-hybrid assays and various derivatives thereof, preferably
reverse two-hybrid assays, are utilized in identifying compounds
that interfere with or disrupt protein-protein interactions between
APOA1 or a homologue, derivative or fragment thereof and an
APOA1-interacting protein or a homologue, derivative or fragment
thereof. In addition, systems such as yeast two-hybrid assays are
also useful in selecting compounds capable of triggering or
initiating, enhancing or stabilizing protein-protein interactions
between APOA1 or a homologue, derivative or fragment thereof and an
APOA1-interacting protein of the present invention or a homologue,
derivative or fragment thereof.
[0023] In a specific embodiment, the screening method includes: (a)
providing in a host cell a first fusion protein having a first
protein which is APOA1 or a homologue or derivative or fragment
thereof, and a second fusion protein having a second protein which
is APOA1-interacting protein as provided in the present invention,
or a homologue or derivative or fragment thereof, wherein a DNA
binding domain is fused to one of the first and second proteins
while a transcription-activating domain is fused to the other of
said first and second proteins; (b) providing in the host cell a
reporter gene, wherein the transcription of the reporter gene is
determined by the interaction between the first protein and the
second protein; (c) allowing the first and second fusion proteins
to interact with each other within the host cell in the presence of
a test compound; and (d) determining the presence or absence of
expression of the reporter gene.
[0024] In addition, the present invention also provides a method
for selecting a compound capable of modulating a protein-protein
interaction between APOA1 and an APOA1-interacting protein in a
protein complex, which comprises the steps of (1) contacting a test
compound with an APOA1-interacting protein or a homologue or
derivative or fragment thereof, and (2) determining whether said
test compound is capable of binding said protein. In a preferred
embodiment, the method further includes testing a selected test
compound capable of binding said protein for its ability to
interfere with a protein-protein interaction between APOA1 and the
APOA1-interacting protein, and optionally further testing the
selected test compound capable of binding said protein for its
ability to modulate cellular activities associated with APOA1
and/or the APOA1-interacting protein.
[0025] The present invention also relates to a virtual screen
method for providing a compound capable of modulating an
interaction between the interacting members in the protein
complexes of the present invention. In one embodiment, the method
comprises the steps of providing atomic coordinates defining a
three-dimensional structure of a protein complex of the present
invention, and designing or selecting compounds capable of
interfering with the interaction between said first protein and
said second protein based on said atomic coordinates. In another
embodiment, the method comprises the steps of providing atomic
coordinates defining a three-dimensional structure of APOA1, or an
APOA1-interacting protein, and designing or selecting compounds
capable of binding APOA1 or the APOA1-interacting protein based on
said atomic coordinates. In preferred embodiments, the method
further includes testing a selected test compound for its ability
to interfere with a protein-protein interaction between APOA1 and
the APOA1-interacting protein, and optionally further testing the
selected test compound for its ability to modulate cellular
activities associated with APOA1 and/or the APOA1-interacting
protein.
[0026] The present invention further provides a composition having
two expression vectors. One vector contains a nucleic acid encoding
APOA1 or a homologue, derivative or fragment thereof. Another
vector contains an APOA1-interacting protein or a homologue,
derivative or fragment thereof. In addition, an expression vector
is also provided containing (1) a first nucleic acid encoding APOA1
or a homologue, derivative or fragment thereof; and (2) a second
nucleic acid encoding an APOA1-interacting protein or a homologue,
derivative or fragment thereof.
[0027] Host cells are also provided comprising the expression
vector(s). In addition, the present invention also provides a host
cell having two expression cassettes. One expression cassette
includes a promoter operably linked to a nucleic acid encoding
APOA1 or a homologue, derivative or fragment thereof. Another
expression cassette includes a promoter operably linked to a
nucleic acid encoding an APOA1-interacting protein or a homologue,
derivative or fragment thereof. Preferably, the expression
cassettes are chimeric expression cassettes with heterologous
promoters included.
[0028] In specific embodiments of the host cells or expression
vectors, one of the two nucleic acids is linked to a nucleic acid
encoding a DNA binding domain, and the other is linked to a nucleic
acid encoding a transcription-activation domain, whereby two fusion
proteins can be encoded.
[0029] In accordance with yet another aspect of the present
invention, methods are provided for modulating the functions and
activities of an APOA1-containing protein complex of the present
invention, or interacting protein members thereof. The methods may
be used in treating or preventing diseases and disorders such as
dementia such as Alzheimer's disease and cardiovascular diseases
such as coronary heart disease, atherosclerosis,
hypercholesterolemia, Tangier disease and amyloidosis. In one
embodiment, the method comprises reducing the protein complex
concentration and/or inhibiting the functional activities of the
protein complex. Alternatively, the concentration and/or activity
of APOA1 or one of the APOA1-interacting proteins may be reduced or
inhibited. Thus, the methods may include administering to a patient
an antibody specific to a protein complex or APOA1 or an APOA1
-interacting protein, an antisense oligo or ribozyme selectively
hybridizable to a gene or mRNA encoding APOA1 or an
APOA1-interacting protein. Also useful is a compound identified in
a screening assay of the present invention capable of disrupting
the interaction between APOA1 and an APOA1-interacting protein, or
inhibiting the activities of APOA1 and/or an APOA1-interacting
protein. In addition, gene therapy methods may also be used in
reducing the expression of the gene(s) encoding APOA1 and/or an
APOA1-interacting protein.
[0030] In another embodiment, the methods for modulating the
functions and activities of an APOA1-containing protein complex of
the present invention or interacting protein members thereof
comprises increasing the protein complex concentration and/or
activating the functional activities of the protein complex.
Alternatively, the concentration and/or activity of one of the
APOA1-interacting proteins or APOA1 may be increased. Thus, a
particular APOA1 -containing protein complex, APOA1 or an
APOA1-interacting protein of the present invention may be
administered directly to a patient. Or, exogenous genes encoding
one or more protein members of an APOA1-containing protein complex
may be introduced into a patient by gene therapy techniques. In
addition, a patient needing treatment or prevention may also be
administered with compounds identified in a screening assay of the
present invention capable of triggering or initiating, enhancing or
stabilizing protein-protein interactions between APOA1 or a
homologue, derivative or fragment thereof and an APOA1-interacting
protein provided in the present invention, or a homologue,
derivative or fragment thereof.
[0031] The foregoing and other advantages and features of the
invention, and the manner in which the same are accomplished, will
become more readily apparent upon consideration of the following
detailed description of the invention taken in conjunction with the
accompanying examples, which illustrate preferred and exemplary
embodiments.
DETAILED DESCRIPTION OF THE INVENTION
1. Definitions
[0032] The terms "polypeptide," "protein," and "peptide" are used
herein interchangeably to refer to amino acid chains in which the
amino acid residues are linked by peptide bonds or modified peptide
bonds. The amino acid chains can be of any length of greater than
two amino acids. Unless otherwise specified, the terms
"polypeptide," "protein," and "peptide" also encompass various
modified forms thereof. Such modified forms may be naturally
occurring modified forms or chemically modified forms. Examples of
modified forms include, but are not limited to, glycosylated forms,
phosphorylated forms, myristoylated forms, palmitoylated forms,
ribosylated forms, acetylated forms, ubiquitinated forms, etc.
Modifications also include intra-molecular crosslinking and
covalent attachment to various moieties such as lipids, flavin,
biotin, polyethylene glycol or derivatives thereof, etc. In
addition, modifications may also include cyclization, branching and
cross-linking. Further, amino acids other than the conventional
twenty amino acids encoded by genes may also be included in a
polypeptide.
[0033] As used herein, the term "interacting" or "interaction"
means that two protein domains, fragments or complete proteins
exhibit sufficient physical affinity to each other so as to bring
the two "interacting" protein domains, fragments or proteins
physically close to each other. An extreme case of interaction is
the formation of a chemical bond that results in continual and
stable proximity of the two entities. Interactions that are based
solely on physical affinities, although usually more dynamic than
chemically bonded interactions, can be equally effective in
co-localizing two proteins. Examples of physical affinities and
chemical bonds include but are not limited to, forces caused by
electrical charge differences, hydrophobicity, hydrogen bonds, van
der Waals force, ionic force, covalent linkages, and combinations
thereof. The state of proximity between the interaction domains,
fragments, proteins or entities may be transient or permanent,
reversible or irreversible. In any event, it is in contrast to and
distinguishable from contact caused by natural random movement of
two entities. Typically, although not necessarily, an "interaction"
is exhibited by the binding between the interaction domains,
fragments, proteins, or entities. Examples of interactions include
specific interactions between antigen and antibody, ligand and
receptor, enzyme and substrate, and the like.
[0034] An "interaction" between two protein domains, fragments or
complete proteins can be determined by a number of methods. For
example, an interaction can be determined by functional assays such
as the two-hybrid systems. Protein-protein interactions can also be
determined by various biophysical and biochemical approaches based
on the affinity binding between the two interacting partners. Such
biochemical methods generally known in the art include, but are not
limited to, protein affinity chromatography, affinity blotting,
immunoprecipitation, and the like. The binding constant for two
interacting proteins, which reflects the strength or quality of the
interaction, can also be determined using methods known in the art.
See Phizicky and Fields, Microbiol. Rev., 59:94-123 (1995).
[0035] As used herein, the term "protein complex" means a composite
unit that is a combination of two or more proteins formed by
interaction between the proteins. Typically, but not necessarily, a
"protein complex" is formed by the binding of two or more proteins
together through specific non-covalent binding interactions.
However, covalent bonds may also be present between the interacting
partners. For instance, the two interacting partners can be
covalently crosslinked so that the protein complex becomes more
stable.
[0036] The term "protein fragment" as used herein means a
polypeptide that represents a portion of a protein. When a protein
fragment exhibits interactions with another protein or protein
fragment, the two entities are said to interact through interaction
domains that are contained within the entities.
[0037] As used herein, the term "domain" means a functional
portion, segment or region of a protein, or polypeptide.
"Interaction domain" refers specifically to a portion, segment or
region of a protein, polypeptide or protein fragment that is
responsible for the physical affinity of that protein, protein
fragment or isolated domain for another protein, protein fragment
or isolated domain.
[0038] The term "isolated" when used in reference to nucleic acids
(which include gene sequences) of this invention is intended to
mean that a nucleic acid molecule is present in a form other than
found in nature in its original environment with respect to its
association with other molecules. For example, since a naturally
existing chromosome includes a long nucleic acid sequence, an
"isolated nucleic acid" as used herein means a nucleic acid
molecule having only a portion of the nucleic acid sequence in the
chromosome but not one or more other portions present on the same
chromosome. Thus, for example, an isolated gene typically includes
no more than 5 kb, preferably no more than 2 kb, more preferably no
more than 1 kb naturally occurring nucleic acid sequence that
immediately flanks the gene in the naturally existing chromosome or
genomic DNA. However, it is noted that an "isolated nucleic acid"
as used herein is distinct from a clone in a conventional library
such as genomic DNA library and cDNA library in that the clones in
a library is still in admixture with almost all the other nucleic
acids in a chromosome or a cell. An isolated nucleic acid can be in
a vector. An isolated nucleic acid can also be part of a
composition so long as the composition is substantially different
from the nucleic acid's original natural environment. In this
respect, an isolated nucleic acid can be in a semi-purified state,
i.e., in a composition having certain natural cellular components,
while it is substantially separated from other naturally occurring
nucleic acids and can be readily detected and/or assayed by
standard molecular biology techniques. Preferably, an "isolated
nucleic acid" is separated from at least 50%, more preferably at
least 75%, most preferably at least 90% of other naturally
occurring nucleic acids.
[0039] The term "isolated nucleic acid" embraces "purified nucleic
acid" which means a specified nucleic acid is in a substantially
homogenous preparation of nucleic acid substantially free of other
cellular components, other nucleic acids, viral materials, or
culture medium, or chemical precursors or by-products associated
with chemical reactions for chemical synthesis of nucleic acids.
Typically, a "purified nucleic acid" can be obtained by standard
nucleic acid purification methods. In a purified nucleic acid,
preferably the specified nucleic acid molecule constitutes at least
75%, preferably at least 85%, and more preferably at least 95% of
the total nucleic acids in the preparation. The term "purified
nucleic acid" also means nucleic acids prepared from a recombinant
host cell (in which the nucleic acids have been recombinantly
amplified and/or expressed) or chemically synthesized nucleic
acids.
[0040] The term "isolated nucleic acid" also encompasses
"recombinant nucleic acid" which is used herein to mean a hybrid
nucleic acid produced by recombinant DNA technology having the
specified nucleic acid molecule covalently linked to one or more
nucleic acid molecules that are not the nucleic acids naturally
flanking the specified nucleic acid. Typically, such one or more
nucleic acid molecules flanking the specified nucleic acid are no
more than 50 kb, preferably no more than 25 kb.
[0041] The term "isolated polypeptide" as used herein means a
polypeptide molecule is present in a form other than found in
nature in its original environment with respect to its association
with other molecules. Typically, an "isolated polypeptide" is
separated from at least 50%, more preferably at least 75%, most
preferably at least 90% of other naturally co-existing polypeptides
in a cell or organism.
[0042] The term "isolated polypeptide" encompasses a "purified
polypeptide" which is used herein to mean a specified polypeptide
is in a substantially homogenous preparation substantially free of
other cellular components, other polypeptides, viral materials, or
culture medium, or when the polypeptide is chemically synthesized,
chemical precursors or by-products associated with the chemical
synthesis. For a purified polypeptide, preferably the specified
polypeptide molecule constitutes at least 75%, preferably at least
85%, and more preferably at least 95% of the total polypeptide in
the preparation. A "purified polypeptide" can be obtained from
natural or recombinant host cells by standard purification
techniques, or by chemically synthesis.
[0043] The term "isolated polypeptide" also encompasses a
"recombinant polypeptide" which is used herein to mean a hybrid
polypeptide produced by recombinant DNA technology or chemical
synthesis having a specified polypeptide molecule covalently linked
to one or more polypeptide molecules that do not naturally flank
the specified polypeptide.
[0044] As used herein, the term "homologue," when used in
connection with a first native protein or fragment thereof that is
discovered, according to the present invention, to interact with a
second native protein or fragment thereof, means a polypeptide that
exhibits an amino acid sequence homology and/or structural
resemblance to the first native interacting protein, or to one of
the interacting domains of the first native protein such that it is
capable of interacting with the second native protein. Typically, a
protein homologue of a native protein may have an amino acid
sequence that is at least 50%, preferably at least 75%, more
preferably at least 80%, 85%, 86%, 87%, 88% or 89%, even more
preferably at least 90%, 91%, 92%, 93% or 94%, and most preferably
95%, 96%, 97%, 98% or 99% identical to the native protein. Examples
of homologues may be the ortholog proteins of other species
including animals, plants, yeast, bacteria, and the like.
Homologues may also be selected by, e.g., mutagenesis in a native
protein. For example, homologues may be identified by site-specific
mutagenesis in combination with assays for detecting
protein-protein interactions, e.g., the yeast two-hybrid system
described below, as will be apparent to skilled artisans apprised
of the present invention. Other techniques for detecting
protein-protein interactions include, e.g., protein affinity
chromatography, affinity blotting, in vitro binding assays, and the
like.
[0045] For the purpose of comparing two different nucleic acid or
polypeptide sequences, one sequence (test sequence) may be
described to be a specific "percent identical to" another sequence
(reference sequence) in the present disclosure. In this respect,
when the length of the test sequence is less than 90% of the length
of the reference sequence, the percentage identity is determined by
the algorithm of Myers and Miller, Bull. Math. Biol., 51:5-37
(1989) and Myers and Miller, Comput. Appl. Biosci., 4(1):11-7
(1988). Specifically, the identity is determined by the ALIGN
program, which is available at http://www2.igh.cnrs.fr maintained
by IGH, Montpellier, FRANCE. The default parameters can be
used.
[0046] Where the length of the test sequence is at least 90% of the
length of the reference sequence, the percentage identity is
determined by the algorithm of Karlin and Altschul, Proc. Natl.
Acad. Sci. USA, 90:5873-77 (1993), which is incorporated into
various BLAST programs. Specifically, the percentage identity is
determined by the "BLAST 2 Sequences" tool, which is available at
http://www.ncbi.nlm.nih.gov/gorf/b12.html. See Tatusova and Madden,
FEMS Microbiol. Lett., 174(2):247-50 (1999). For pairwise DNA-DNA
comparison, the BLASTN 2.1.2 program is used with default
parameters (Match: 1; Mismatch: -2; Open gap: 5 penalties;
extension gap: 2 penalties; gap x_dropoff: 50; expect: 10; and word
size: 11, with filter). For pairwise protein-protein sequence
comparison, the BLASTP 2.1.2 program is employed using default
parameters (Matrix: BLOSUM62; gap open: 11; gap extension: 1;
x_dropoff: 15; expect: 10.0; and wordsize: 3, with filter).
[0047] The term "derivative," when used in connection with a first
native protein (or fragment thereof) that is discovered, according
to the present invention, to interact with a second native protein
(or fragment thereof), means a modified form of the first native
protein prepared by modifying the side chain groups of the first
native protein without changing the amino acid sequence of the
first native protein. The modified form, i.e., the derivative
should be capable of interacting with the second native protein.
Examples of modified forms include glycosylated forms,
phosphorylated forms, myristylated forms, ribosylated forms,
ubiquitinated forms, and the like. Derivatives also include hybrid
or fusion proteins containing a native protein or a fragment
thereof. Methods for preparing such derivative forms should be
apparent to skilled artisans. The prepared derivatives can be
easily tested for their ability to interact with the native
interacting partner using techniques known in the art, e.g.,
protein affinity chromatography, affinity blotting, in vitro
binding assays, yeast two-hybrid assays, and the like.
[0048] The term "isolated protein complex" means a protein complex
present in a composition or environment that is different from that
found in nature--in its native or original cellular or body
environment. Preferably, an "isolated protein complex" is separated
from at least 50%, more preferably at least 75%, most preferably at
least 90% of other naturally co-existing cellular or tissue
components. Thus, an "isolated protein complex" may also be a
naturally existing protein complex in an artificial preparation or
a non-native host cell. An "isolated protein complex" may also be a
"purified protein complex", that is, a substantially purified form
in a substantially homogenous preparation substantially free of
other cellular components, other polypeptides, viral materials, or
culture medium, or, when the protein components in the protein
complex are chemically synthesized, free of chemical precursors or
by-products associated with the chemical synthesis. A "purified
protein complex" typically means a preparation containing
preferably at least 75%, more preferably at least 85%, and most
preferably at least 95% a particular protein complex. A "purified
protein complex" may be obtained from natural or recombinant host
cells or other body samples by standard purification techniques, or
by chemical synthesis.
[0049] The terms "hybrid protein," "hybrid polypeptide," "hybrid
peptide," "fusion protein," "fusion polypeptide," and "fusion
peptide" are used herein interchangeably to mean a non-naturally
occurring protein having a specified polypeptide molecule
covalently linked to one or more polypeptide molecules that do not
naturally link to the specified polypeptide. Thus, a "hybrid
protein" may be two naturally occurring proteins or fragments
thereof linked together by a covalent linkage. A "hybrid protein"
may also be a protein formed by covalently linking two artificial
polypeptides together. Typically but not necessarily, the two or
more polypeptide molecules are linked or "fused" together by a
peptide bond forming a single non-branched polypeptide chain.
[0050] The term "antibody" as used herein encompasses both
monoclonal and polyclonal antibodies that fall within any antibody
classes, e.g., IgG, IgM, IgA, or derivatives thereof. The term
"antibody" also includes antibody fragments including, but not
limited to, Fab, F(ab').sub.2, and conjugates of such fragments,
and single-chain antibodies comprising an antigen recognition
epitope. In addition, the term "antibody" also means humanized
antibodies, including partially or fully humanized antibodies. An
antibody may be obtained from an animal, or from a hybridoma cell
line producing a monoclonal antibody, or obtained from cells or
libraries recombinantly expressing a gene encoding a particular
antibody.
[0051] The term "selectively immunoreactive" as used herein means
that an antibody is reactive thus binds to a specific protein or
protein complex, but not other similar proteins or fragments or
components thereof.
[0052] The term "activity" when used in connection with proteins or
protein complexes means any physiological or biochemical activities
displayed by or associated with a particular protein or protein
complex including but not limited to activities exhibited in
biological processes and cellular functions, ability to interact
with or bind another molecule or a moiety thereof, binding affinity
or specificity to certain molecules, in vitro or in vivo stability
(e.g., protein degradation rate, or in the case of protein
complexes ability to maintain the form of protein complex),
antigenicity and immunogenecity, enzymatic activities, etc. Such
activities may be detected or assayed by any of a variety of
suitable methods as will be apparent to skilled artisans.
[0053] The term "compound" as used herein encompasses all types of
organic or inorganic molecules, including but not limited proteins,
peptides, polysaccharides, lipids, nucleic acids, small organic
molecules, inorganic compounds, and derivatives thereof.
[0054] As used herein, the term "interaction antagonist" means a
compound that interferes with, blocks, disrupts or destabilizes a
protein-protein interaction; blocks or interferes with the
formation of a protein complex; or destabilizes, disrupts or
dissociates an existing protein complex.
[0055] The term "interaction agonist" as used herein means a
compound that triggers, initiates, propagates, nucleates, or
otherwise enhances the formation of a protein-protein interaction;
triggers, initiates, propagates, nucleates, or otherwise enhances
the formation of a protein complex; or stabilizes an existing
protein complex.
[0056] Unless otherwise specified, the term "APOA1" as used herein
means the human APOA1 protein. The usage for naming other proteins
should be similar unless otherwise specified in the present
disclosure.
2. Protein Complexes
[0057] Novel protein-protein interactions have been discovered and
confirmed using yeast two-hybrid systems. In particular, it has
been discovered that APOA1 specifically interacts with proteins
including PRA1, GOLGIN-84, Syntaxin 2, APOB and FLJ20724. Specific
fragments capable of conferring interacting properties on APOA1,
and the APOA1 -interacting proteins have also been identified,
which are summarized in Table 1. The GenBank Reference Numbers for
the cDNA sequences encoding APOA1, and the APOA1 -interacting
proteins are noted in Table 1 below.
1TABLE 1 Binding Regions of APOA1 and Its Interacting Partners Bait
Protein Prey Proteins Name and Amino Acid GenBank Amino Acid
GenBank Coordinates Accession Coordinates Accession No. Start Stop
Names Nos. Start Stop Apolipoprotein A-I 23 267 golgi NM_005113 534
731 ("APOA1") 23 267 autoantigen, 84 563 731 (GenBank 106 267 kD
protein 512 726 Accession No. ("Golgin-84") NM_000039) 106 267
apolipoprotein X04506 4307 4522 B-100 ("APOB") 106 267 syntaxin 2
D14582 156 261 ("STX2") 106 267 prenylated Rab NM_006423 1 185*
acceptor 1 ("PRA1") 106 267 hypothetical NM_017942 162 248 protein
FLJ20724 ("FLJ20724")
2.1. Biological Significance
[0058] We have demonstrated an interaction between apolipoprotein
A-I (APOA1) and a prenylated Rab acceptor 1 (PRA1) in a yeast
two-hybrid search of a liver library. APOA1 is synthesized and
secreted by the liver and small intestine, and is the major protein
component of HDL. It is required for HDL formation and reverse
cholesterol transport (cholesterol efflux) from tissues to the
liver. APOA1 functions as the acceptor of cholesterol from
ABCA1-expressing cells as well as a cofactor for lecithin
cholesterol acyltransferase (LCAT). A variant of APOA1 was found
that fails to associate with HDL resulting in the absence of HDL,
the accumulation of cholesteryl esters, and subsequent development
of Tangier disease. Schmitz et al., Proc. Nat. Acad. Sci., 80:6081
(1983). Autosomal dominant non-neuropathic systemic amyloidosis is
also the result of mutations in the APOA1 gene. Soutar et al.,
Proc. Nat. Acad. Sci., 89:7389 (1992). PRA 1 (Rab acceptor 1 or
RABAC1) was previously identified as an interactor of activated
(GTP-bound) prenylated Rab. Bucci et al., Biochem. Biophys, Res.
Commun., 58:657 (1999). Rab proteins are members of the small
GTPase Ras superfamily that are required in intracellular vesicle
trafficking. They are believed to be required for the assembly of
the SNARE fusion complex and to ensure proper docking and fusion of
transport vesicles. S.o slashed.gaard et al., Cell, 78:937-948
(1994).
[0059] Northern blot analysis indicates that PRA1 is expressed
ubiquitously, although dot-blot analysis indicates that it may be
most highly expressed in placenta, pituitary gland, kidney, and
stomach. PRA1 contains several putative transmembrane domains.
[0060] Figueroa et al., J. Biol. Chem., 276: 28219-28225 (2001)
suggested that PRA1acts as an escort protein for small GTPases by
binding to the hydrophobic isoprenoid moieties of the small GTPases
and facilitates their trafficking through the endomembrane system.
In addition, PRA1 also binds specifically to the synaptic vesicle
protein VAMP2 (or synaptobrevin II) through the proline-rich domain
of VAMP2. Martincic et al., J. Biol. Chem., 272:26991-26998
(1997).
[0061] The APOA1-PRA1 interaction may be relevant to the secretion
of APOA1 or the interaction of APOA1 with membranes during
cholesterol efflux. In particular, the interaction may be required
for cholesterol efflux and thus, may contribute to the reduction of
body cholesterol level. Thus, modulation of the interaction, in
particular, enhancement of the interaction may prove to be
beneficial to cholesterol-related diseases such as coronary heart
diseases and dementia such as Alzheimer's disease.
[0062] In addition, we have also demonstrated an interaction
between APOA1 and golgi autoantigen 84 KD protein (GOLGIN-84),
which is another protein involved in intracellular vesicle
trafficking. This interaction may also be involved in the secretion
of APOA1 or the interaction of APOA1 with membranes during
cholesterol efflux. Modulation of this interaction may also be
effective in ameliorating coronary heart diseases and Alzheimer's
disease.
[0063] With a fragment of APOA1 comprising the C-terminal half of
the protein (residues 106-268) a fragment (residues 156-261) of
syntaxin was isolated. Syntaxin 2 belongs to the family of SNARE
proteins involved in vesicle fusions. Syntaxin 2 has a cytosolic
coiled coil domain and a C-terminal transmembrane domain. Several
splice variants were identified that have different C-termini, one
variant lacking the transmembrane domain. Quinones et al., J. Cell
Sci, 112:4291-4304 (1999). The APOA1-syntaxin 2 interaction may be
relevant to the secretion of APOA1 or the interaction of APOA1 with
membranes during cholesterol efflux. Modulation of this interaction
may also be effective in ameliorating coronary heart diseases and
Alzheimer's disease.
[0064] With a fragment of APOA1 comprising the C-terminal half of
the protein (residues 106-268) a C-terminal fragment (residues
4307-4522) of apolipoprotein B-100 (APOB) was isolated. The
4563-residue APOB protein is the major protein component of
chylomicrons, VLDL, and LDL and mediates interaction with the LDL
receptor family. Defects in APOB can lead to coronary heart disease
due to increased plasma levels of LDL cholesterol. A portion of
esterified cholesterol is transferred from HDL to LDL particles via
cholesteryl ester transfer protein (CETP). The underlying physical
interaction between HDL and LDL particles may be mediated by direct
protein interaction between their respective apolipoproteins, APOA1
and APOB. Disruption of the interaction may lead to the inhibition
of the transfer of esterified cholesterol from HDL to LDL
particles.
[0065] With a fragment of APOA1 comprising the C-terminal half of
the protein (residues 106-268) a fragment (residues 162-248) of
FLJ20724 was isolated. The 482-residue FLJ20724 protein, also known
as BTB domain-containing protein (BTBD1), contains a BTB/POZ domain
which is found in some zinc finger proteins and in the kelch family
of actin-associated proteins. Carim-Todd et al., Gene
262:275-281(2001). The interaction between APOA1 and FLJ20724
suggests that FLJ20724 may also be involved in cholesterol
transport and lipid metabolism.
2.2. Protein Complexes
[0066] Accordingly, the present invention provides protein
complexes formed between APOA1 and one or more APOA1-interacting
proteins selected from the group consisting of PRA1, GOLGIN-84,
Syntaxin 2, APOB and FLJ20724. The present invention also provides
protein complexes formed from the interaction between homologues,
derivatives or fragments of APOA1 and one or more of the
APOA1-interacting proteins in accordance with the present
invention. In addition, the present invention further encompasses
protein complexes having APOA1 and homologues, derivatives or
fragments of one or more of the APOA1-interacting proteins in
accordance with the present invention. In yet another embodiment,
protein complexes are provided having homologues, derivatives or
fragments of APOA1 and homologues, derivatives or fragments of one
or more of the APOA1-interacting proteins in accordance with the
present invention. In other words, one or more of the interacting
protein members of a protein complex of the present invention may
be a native protein or a homologue, derivative or fragment of a
native protein.
[0067] Thus, for example, one interacting partner in a protein
complex can be a complete native APOA1, an APOA1 homologue capable
of interacting with, e.g., PRA1, an APOA1 derivative, a derivative
of the APOA1 homologue, an APOA1 fragment capable of interacting
with PRA1 (APOA1 fragment(s) containing the coordinates shown in
Table 1), a derivative of the APOA1 fragment, or a fusion protein
containing (1) complete native APOA1, (2) an APOA1 homologue
capable of interacting with PRA1 or (3) an APOA1 fragment capable
of interacting with PRA1. Besides native PRA1, useful interacting
partners for APOA1 or a homologue or derivative or fragment thereof
also include homologues of PRA1 capable of interacting with APOA1,
derivatives of the native or homologue PRA1 capable of interacting
with APOA1, fragments of the PRA1capable of interacting with APOA1
(e.g., a fragment containing the identified interacting regions
shown in Table 1), derivatives of the PRA1 fragments, or fusion
proteins containing (1) a complete PRA1, (2) a PRA1 homologue
capable of interacting with APOA1 or (3) a PRA1 fragment capable of
interacting with APOA1.
[0068] PRA1 fragments capable of interacting with APOA1 can be
identified by the combination of molecular engineering of a
PRA1-encoding nucleic acid and a method for testing protein-protein
interaction. For example, the coordinates in Table 1 can be used as
starting points and various PRA1 fragments falling within the
coordinates can be generated by deletions from either or both ends
of the coordinates. The resulting fragments can be tested for their
ability to interact with APOA1 using any methods known in the art
for detecting protein-protein interactions (e.g., yeast two-hybrid
method). Alternatively, various PRA1 fragments can be made by
chemical synthesis. The PRA1 fragments can then be tested for its
ability to interact with APOA1 using any method known in the art
for detecting protein-protein interactions. Examples of such
methods include protein affinity chromatography, affinity blotting,
in vitro binding assays, yeast two-hybrid assays, and the like.
Likewise, APOA1 fragments capable of interacting with PRA1 can also
be identified in a similar manner.
[0069] Other protein complexes can be formed in a similar manner
based on interactions between APOA1 and its other interacting
partners discovered according to the present invention or
homologues, derivatives or fragments of such other interacting
partners. In addition, protein complexes containing APOA1 and two
or more members of the group of PRA1, GOLGIN-84, Syntaxin 2, APOB
and FLJ20724 or homologues, derivatives, or fragments thereof can
also be formed.
[0070] In a specific embodiment of the protein complex of the
present invention, two or more interacting partners (APOA1 and one
or more proteins selected from the group consisting of PRA1,
GOLGIN-84, Syntaxin 2, APOB and FLJ20724, or homologues,
derivatives or fragments thereof) are directly fused together, or
covalently linked together through a peptide linker, forming a
hybrid protein having a single unbranched polypeptide chain. Thus,
the protein complex may be formed by "intramolecular" interactions
between two portions of the hybrid protein. Again, one or both of
the fused or linked interacting partners in this protein complex
may be a native protein or a homologue, derivative or fragment of a
native protein.
[0071] The protein complexes of the present invention can also be
in a modified form. For example, an antibody selectively
immunoreactive with the protein complex can be bound to the protein
complex. In another example, a non-antibody modulator capable of
enhancing the interaction between the interacting partners in the
protein complex may be included. Alternatively, the protein members
in the protein complex may be cross-linked for purposes of
stabilization. Various crosslinking methods may be used. For
example, a bifunctional reagent in the form of R-S-S-R' may be used
in which the R and R' groups can react with certain amino acid side
chains in the protein complex forming covalent linkages. See e.g.,
Traut et al., in Creighton ed., Protein Function: A Practical
Approach, IRL Press, Oxford, 1989; Baird et al., J. Biol. Chem.,
251:6953-6962 (1976). Other useful crosslinking agents include,
e.g., Denny-Jaffee reagent, a heterbiofunctional photoactivable
moiety cleavable through an azo linkage (See Denny et al., Proc.
Natl. Acad. Sci. USA, 81:5286-5290 (1984)), and
.sup.125I-{S-[N-(3-iodo-4-azidosalicy-
l)cysteaminyl]-2-thiopyridine}, a cysteine-specific
photocrosslinking reagent (see Chen et al., Science, 265:90-92
(1994)).
[0072] The above-described protein complexes may further include
any additional components, e.g., other proteins, nucleic acids,
lipid molecules, monosaccharides or polysaccharides, ions, etc.
2.3. Methods of Preparing Protein Complexes
[0073] The protein complex of the present invention can be prepared
by a variety of methods. Specifically, a protein complex can be
isolated directly from an animal tissue sample, preferably a human
tissue sample containing the protein complex. Alternatively, a
protein complex can be purified from host cells that recombinantly
express the members of the protein complex. As will be apparent to
a skilled artisan, a protein complex can be prepared from a tissue
sample or recombinant host cells by coimmunoprecipitation using an
antibody immunoreactive with an interacting protein partner, or
preferably an antibody selectively immunoreactive with the protein
complex as will be discussed in detail below.
[0074] The antibodies can be monoclonal or polyclonal.
Coimmunoprecipitation is a commonly used method in the art for
isolating or detecting bound proteins. In this procedure, generally
a serum sample or tissue or cell lysate is admixed with a suitable
antibody. The protein complex bound to the antibody is precipitated
and washed. The bound protein complexes are then eluted.
[0075] Alternatively, immunoaffinity chromatography and
immunobloting techniques may also be used in isolating the protein
complexes from native tissue samples or recombinant host cells
using an antibody immunoreactive with an interacting protein
partner, or preferably an antibody selectively immunoreactive with
the protein complex. For example, in protein immunoaffinity
chromatography, the antibody is covalently or non-covalently
coupled to a matrix (e.g., Sepharose), which is then packed into a
column. Extract from a tissue sample, or lysate from recombinant
cells is passed through the column where it contacts the antibodies
attached to the matrix. The column is then washed with a low-salt
solution to wash away the unbound or loosely (non-specifically)
bound components. The protein complexes that are retained in the
column can be then eluted from the column using a high-salt
solution, a competitive antigen of the antibody, a chaotropic
solvent, or sodium dodecyl sulfate (SDS), or the like. In
immunoblotting, crude proteins samples from a tissue sample extract
or recombinant host cell lysate are fractionated by polyacrylamide
gel electrophoresis (PAGE) and then transferred to a membrane,
e.g., nitrocellulose. Components of the protein complex can then be
located on the membrane and identified by a variety of techniques,
e.g., probing with specific antibodies.
[0076] In another embodiment, individual interacting protein
partners may be isolated or purified independently from tissue
samples or recombinant host cells using similar methods as
described above. The individual interacting protein partners are
then combined under conditions conducive to their interaction
thereby forming a protein complex of the present invention. It is
noted that different protein-protein interactions may require
different conditions. As a starting point, for example, a buffer
having 20 mM Tris-HCl, pH 7.0 and 500 mM NaCl may be used. Several
different parameters may be varied, including temperature, pH, salt
concentration, reducing agent, and the like. Some minor degree of
experimentation may be required to determine the optimum incubation
condition, this being well within the capability of one skilled in
the art once apprised of the present disclosure.
[0077] In yet another embodiment, the protein complex of the
present invention may be prepared from tissue samples or
recombinant host cells or other suitable sources by protein
affinity chromatography or affinity blotting. That is, one of the
interacting protein partners is used to isolate the other
interacting protein partner(s) by binding affinity thus forming
protein complexes. Thus, an interacting protein partner prepared by
purification from tissue samples or by recombinant expression or
chemical synthesis may be bound covalently or non-covalently to a
matrix, e.g., Sepharose, which is then packed into a chromatography
column. The tissue sample extract or cell lysate from the
recombinant cells can then be contacted with the bound protein on
the matrix. A low-salt solution is used to wash off the unbound or
loosely bound components, and a high-salt solution is then employed
to elute the bound protein complexes in the column. In affinity
blotting, crude protein samples from a tissue sample or recombinant
host cell lysate can be fractionated by polyacrylamide gel
electrophoresis (PAGE) and then transferred to a membrane, e.g.,
nitrocellulose. The purified interacting protein member is then
bound to its interacting protein partner(s) on the membrane forming
protein complexes, which are then isolated from the membrane.
[0078] It will be apparent to skilled artisans that any recombinant
expression methods may be used in the present invention for
purposes of expressing the protein complexes or individual
interacting proteins. Generally, a nucleic acid encoding an
interacting protein member can be introduced into a suitable host
cell. For purposes of forming a recombinant protein complex within
a host cell, nucleic acids encoding two or more interacting protein
members should be introduced into the host cell.
[0079] Typically, the nucleic acids, preferably in the form of DNA,
are incorporated into a vector to form expression vectors capable
of directing the production of the interacting protein member(s)
once introduced into a host cell. Many types of vectors can be used
for the present invention. Methods for the construction of an
expression vector for purposes of this invention should be apparent
to skilled artisans apprised of the present disclosure. See
generally, Current Protocols in Molecular Biology, Vol. 2, Ed.
Ausubel, et al., Greene Publish. Assoc. & Wiley Interscience,
Ch. 13, 1988; Glover, DNA Cloning, Vol. II, IRL Press, Wash., D.C.,
Ch. 3, 1986; Bitter, et al., in Methods in Enzymology 153:516-544
(1987); The Molecular Biology of the Yeast Saccharomyces, Eds.
Strathern et al., Cold Spring Harbor Press, Vols. I and II, 1982;
and Sambrook et al., Molecular Cloning: A Laboratory Manual, Cold
Spring Harbor Press, 1989.
[0080] Generally, the expression vectors include an expression
cassette having a promoter operably linked to a DNA encoding an
interacting protein member. The promoter can be a native promoter,
i.e., the promoter found in naturally occurring cells to be
responsible for the expression of the interacting protein member in
the cells. Alternatively, the expression cassette can be a chimeric
one, i.e., having a heterologous promoter that is not the native
promoter responsible for the expression of the interacting protein
member in naturally occurring cells. The expression vector may
further include an origin of DNA replication for the replication of
the vectors in host cells. Preferably, the expression vectors also
include a replication origin for the amplification of the vectors
in, e.g., E. coli, and selection marker(s) for selecting and
maintaining only those host cells harboring the expression vectors.
Additionally, the expression cassettes preferably also contain
inducible elements, which function to control the transcription
from the DNA encoding an interacting protein member. Other
regulatory sequences such as transcriptional enhancer sequences and
translation regulation sequences (e.g., Shine-Dalgarno sequence)
can also be operably included in the expression cassettes.
Termination sequences such as the polyadenylation signals from
bovine growth hormone, SV40, lacZ and AcMNPV polyhedral protein
genes may also be operably linked to the DNA encoding an
interacting protein member in the expression cassettes. An epitope
tag coding sequence for detection and/or purification of the
expressed protein can also be operably linked to the DNA encoding
an interacting protein member such that a fusion protein is
expressed. Examples of useful epitope tags include, but are not
limited to, influenza virus hemagglutinin (HA), Simian Virus 5
(V5), polyhistidine (6xHis), c-myc, lacZ, GST, and the like.
Proteins with polyhistidine tags can be easily detected and/or
purified with Ni affinity columns, while specific antibodies
immunoreactive with many epitope tags are generally commercially
available. The expression vectors may also contain components that
direct the expressed protein extracellularly or to a particular
intracellular compartment. Signal peptides, nuclear localization
sequences, endoplasmic reticulum retention signals, mitochondrial
localization sequences, myristoylation signals, palmitoylation
signals, and transmembrane sequences are example of optional vector
components that can determine the destination of expressed
proteins. When it is desirable to express two or more interacting
protein members in a single host cell, the DNA fragments encoding
the interacting protein members may be incorporated into a single
vector or different vectors.
[0081] The thus constructed expression vectors can be introduced
into the host cells by any techniques known in the art, e.g., by
direct DNA transformation, microinjection, electroporation, viral
infection, lipofection, gene gun, and the like. The expression of
the interacting protein members may be transient or stable. The
expression vectors can be maintained in host cells in an
extrachromosomal state, i.e., as self-replicating plasmids or
viruses. Alternatively, the expression vectors can be integrated
into chromosomes of the host cells by conventional techniques such
as selection of stable cell lines or site-specific recombination.
In stable cell lines, at least the expression cassette portion of
the expression vector is integrated into a chromosome of the host
cells.
[0082] The vector construct can be designed to be suitable for
expression in various host cells, including but not limited to
bacteria, yeast cells, plant cells, insect cells, and mammalian and
human cells. Methods for preparing expression vectors for
expression in different host cells should be apparent to a skilled
artisan.
[0083] Homologues and fragments of the native interacting protein
members can also be easily expressed using the recombinant methods
described above. For example, to express a protein fragment, the
DNA fragment incorporated into the expression vector can be
selected such that it only encodes the protein fragment. Likewise,
a specific hybrid protein can be expressed using a recombinant DNA
encoding the hybrid protein. Similarly, a homologue protein may be
expressed from a DNA sequence encoding the homologue protein. A
homologue-encoding DNA sequence may be obtained by manipulating the
native protein-encoding sequence using recombinant DNA techniques.
For this purpose, random or site-directed mutagenesis can be
conducted using techniques generally known in the art. To make
protein derivatives, for example, the amino acid sequence of a
native interacting protein member may be changed in predetermined
manners by site-directed DNA mutagenesis to create or remove
consensus sequences for, e.g., phosphorylation by protein kinases,
glycosylation, ribosylation, myristolation, palmytoylation,
ubiquitination, and the like. Alternatively, non-natural amino
acids can be incorporated into an interacting protein member during
the synthesis of the protein in recombinant host cells. For
example, photoreactive lysine derivatives can be incorporated into
an interacting protein member during translation by using a
modified lysyl-tRNA. See, e.g., Wiedmann et al., Nature,
328:830-833 (1989); Musch et al., Cell, 69:343-352 (1992). Other
photoreactive amino acid derivatives can also be incorporated in a
similar manner. See, e.g., High et al., J. Biol. Chem.,
368:28745-28751 (1993). Indeed, the photoreactive amino acid
derivatives thus incorporated into an interacting protein member
can function to cross-link the protein to its interacting protein
partner in a protein complex under predetermined conditions.
[0084] In addition, derivatives of the native interacting protein
members of the present invention can also be prepared by chemically
linking certain moieties to amino acid side chains of the native
proteins.
[0085] If desired, the homologues and derivatives thus generated
can be tested to determine whether they are capable of interacting
with their intended partners to form protein complexes. Testing can
be conducted by e.g., the yeast two-hybrid system or other methods
known in the art for detecting protein-protein interaction.
[0086] A hybrid protein as described above having APOA1 or a
homologue, derivative, or fragment thereof covalently linked by a
peptide bond or a peptide linker to a protein selected from the
group consisting of PRA1, GOLGIN-84, Syntaxin 2, APOB and FLJ20724
or a homologue, derivative, or fragment thereof, can be expressed
recombinantly from a chimeric nucleic acid, e.g., a DNA or mRNA
fragment encoding the fusion protein. Accordingly, the present
invention also provides a nucleic acid encoding the hybrid protein
of the present invention. In addition, an expression vector having
incorporated therein a nucleic acid encoding the hybrid protein of
the present invention is also provided. The methods for making such
chimeric nucleic acids and expression vectors containing them
should be apparent to skilled artisans apprised of the present
disclosure.
2.4. Protein Microchip
[0087] In accordance with another embodiment of the present
invention, a protein microchip or microarray is provided having one
or more of the protein complexes and/or antibodies selectively
immunoreactive with the protein complexes of the present invention.
Protein microarrays are becoming increasingly important in both
proteomics research and protein-based detection and diagnosis of
diseases. The protein microarrays in accordance with this
embodiment of the present invention will be useful in a variety of
applications including, e.g., large-scale or high-throughput
screening for compounds capable of binding to the protein complexes
or modulating the interactions between the interacting protein
members in the protein complexes.
[0088] The protein microarray of the present invention can be
prepared in a number of methods known in the art. An example of a
suitable method is that disclosed in MacBeath and Schreiber,
Science, 289:1760-1763 (2000). Essentially, glass microscope slides
are treated with an aldehyde-containing silane reagent
(SuperAldehyde Substrates purchased from TeleChem International,
Cupertino, Calif.). Nanoliter volumes of protein samples in a
phosphate-buffered saline with 40% glycerol are then spotted onto
the treated slides using a high-precision contact-printing robot.
After incubation, the slides are immersed in a bovine serum albumin
(BSA)-containing buffer to quench the unreacted aldehydes and to
form a BSA layer that functions to prevent non-specific protein
binding in subsequent applications of the microchip. Alternatively,
as disclosed in MacBeath and Schreiber, proteins or protein
complexes of the present invention can be attached to a BSA-NHS
slide by covalent linkages. BSA-NHS slides are fabricated by first
attaching a molecular layer of BSA to the surface of glass slides
and then activating the BSA with N,N'-disuccinimidyl carbonate. As
a result, the amino groups of the lysine, aspartate, and glutamate
residues on the BSA are activated and can form covalent urea or
amide linkages with protein samples spotted on the slides. See
MacBeath and Schreiber, Science, 289:1760-1763 (2000).
[0089] Another example of a useful method for preparing the protein
microchip of the present invention is that disclosed in PCT
Publication Nos. WO 00/4389A2 and WO 00/04382, both of which are
assigned to Zyomyx and are incorporated herein by reference. First,
a substrate or chip base is covered with one or more layers of thin
organic film to eliminate any surface defects, insulate proteins
from the base materials, and to ensure uniform protein array. Next,
a plurality of protein-capturing agents (e.g., antibodies,
peptides, etc.) are arrayed and attached to the base that is
covered with the thin film. Proteins or protein complexes can then
be bound to the capturing agents forming a protein microarray. The
protein microchips are kept in flow chambers with an aqueous
solution.
[0090] The protein microarray of the present invention can also be
made by the method disclosed in PCT Publication No. WO 99/36576
assigned to Packard Bioscience Company, which is incorporated
herein by reference. For example, a three-dimensional hydrophilic
polymer matrix, i.e., a gel, is first dispensed on a solid
substrate such as a glass slide. The polymer matrix gel is capable
of expanding or contracting and contains a coupling reagent that
reacts with amine groups. Thus, proteins and protein complexes can
be contacted with the matrix gel in an expanded aqueous and porous
state to allow reactions between the amine groups on the protein or
protein complexes with the coupling reagents thus immobilizing the
proteins and protein complexes on the substrate. Thereafter, the
gel is contracted to embed the attached proteins and protein
complexes in the matrix gel.
[0091] Alternatively, the proteins and protein complexes of the
present invention can be incorporated into a commercially available
protein microchip, e.g., the ProteinChip System from Ciphergen
Biosystems Inc., Palo Alto, Calif. The ProteinChip System comprises
metal chips having a treated surface, which interact with proteins.
Basically, a metal chip surface is coated with a silicon dioxide
film. The molecules of interest such as proteins and protein
complexes can then be attached covalently to the chip surface via a
silane coupling agent.
[0092] The protein microchips of the present invention can also be
prepared with other methods known in the art, e.g., those disclosed
in U.S. Pat. Nos. 6,087,102, 6,139,831, 6,087,103; PCT Publication
Nos. WO 99/60156, WO 99/39210, WO 00/54046, WO 00/53625, WO
99/51773, WO 99/35289, WO 97/42507, WO 01/01142, WO 00/63694, WO
00/61806, WO 99/61148, WO 99/40434, all of which are incorporated
herein by reference.
3. Antibodies
[0093] In accordance with another aspect of the present invention,
an antibody immunoreactive against a protein complex of the present
invention is provided. In one embodiment, the antibody is
selectively immunoreactive with a protein complex of the present
invention. Specifically, the phrase "selectively immunoreactive
with a protein complex" as used herein means that the
immunoreactivity of the antibody of the present invention with the
protein complex is substantially higher than that with the
individual interacting members of the protein complex so that the
binding of the antibody to the protein complex is readily
distinguishable from the binding of the antibody to the individual
interacting member proteins based on the strength of the binding
affinities. Preferably, the binding constants differ by a magnitude
of at least 2 fold, more preferably at least 5 fold, even more
preferably at least 10 fold, and most preferably at least 100 fold.
In a specific embodiment, the antibody is not substantially
immunoreactive with the interacting protein members of the protein
complex.
[0094] The antibody of the present invention can be readily
prepared using procedures generally known in the art. See, e.g.,
Harlow and Lane, Antibodies: A Laboratory Manual, Cold Spring
Harbor Press, 1988. Typically, the protein complex against which
the antibody to be generated will be immunoreactive is used as the
antigen for the purpose of producing immune response in a host
animal. In one embodiment, the protein complex used consists the
native proteins. Preferably, the protein complex includes only the
interaction domain(s) of APOA1 and the interaction domain(s) of one
or more proteins selected from the group consisting of PRA1,
GOLGIN-84, Syntaxin 2, APOB and FLJ20724. As a result, a greater
portion of the total antibodies may be selectively immunoreactive
with the protein complexes. The interaction domains can be selected
from, e.g., those regions summarized in Table 1. In addition,
various techniques known in the art for predicting epitopes may
also be employed to design antigenic peptides based on the
interacting protein members in a protein complex of the present
invention to increase the possibility of producing an antibody
selectively immunoreactive with the protein complex. Suitable
epitope-prediction computer programs include, e.g., MacVector from
International Biotechnologies, Inc. and Protean from DNAStar.
[0095] In a specific embodiment, a hybrid protein as described
above in Section 2.1 is used as an antigen which has APOA1 or a
homologue, derivative, or fragment thereof covalently linked by a
peptide bond or a peptide linker to a protein selected from the
group consisting of PRA1, GOLGIN-84, Syntaxin 2, APOB and FLJ20724
or a homologue, derivative, or fragment thereof. In a preferred
embodiment, the hybrid protein consists of two interacting domains
selected from the regions identified in Table 1, or homologues or
derivatives thereof, covalently linked together by a peptide bond
or a linker molecule.
[0096] The antibody of the present invention can be a polyclonal
antibody to a protein complex of the present invention. To produce
the polyclonal antibody, various animal hosts can be employed,
including, e.g., mice, rats, rabbits, goats, guinea pigs, hamsters,
etc. A suitable antigen which is a protein complex of the present
invention or a derivative thereof as described above can be
administered directly to a host animal to illicit immune reactions.
Alternatively, it can be administered together with a carrier such
as keyhole limpet hemocyanin (KLH), bovine serum albumin (BSA),
ovalbumin, and Tetanus toxoid. Optionally, the antigen is
conjugated to a carrier by a coupling agent such as carbodiimide,
glutaraldehyde, and MBS. Any conventional adjuvants may be used to
boost the immune response of the host animal to the protein complex
antigen. Suitable adjuvants known in the art include but are not
limited to Complete Freund's Adjuvant (which contains killed
mycobacterial cells and mineral oil), incomplete Freund's Adjuvant
(which lacks the cellular components), aluminum salts, MF59 from
Biocine, monophospholipid, synthetic trehalose dicorynomycolate
(TDM) and cell wall skeleton (CWS) both from Corixa Corp., Seattle,
Wash., non-ionic surfactant vesicles (NISV) from Proteus
International PLC, Cheshire, U.K., and saponins. The antigen
preparation can be administered to a host animal by subcutaneous,
intramuscular, intravenous, intradermal, or intraperitoneal
injection, or by injection into a lymphoid organ.
[0097] The antibodies of the present invention may also be
monoclonal. Such monoclonal antibodies may be developed using any
conventional techniques known in the art. For example, the popular
hybridoma method disclosed in Kohler and Milstein, Nature,
256:495-497 (1975) is now a well-developed technique that can be
used in the present invention. See U.S. Pat. No. 4,376,110, which
is incorporated herein by reference. Essentially, B-lymphocytes
producing a polyclonal antibody against a protein complex of the
present invention can be fused with myeloma cells to generate a
library of hybridoma clones. The hybridoma population is then
screened for antigen binding specificity and also for
immunoglobulin class (isotype). In this manner, pure hybridoma
clones producing specific homogenous antibodies can be selected.
See generally, Harlow and Lane, Antibodies: A Laboratory Manual,
Cold Spring Harbor Press, 1988. Alternatively, other techniques
known in the art may also be used to prepare monoclonal antibodies,
which include but are not limited to the EBV hybridoma technique,
the human N-cell hybridoma technique, and the trioma technique.
[0098] In addition, antibodies selectively immunoreactive with a
protein complex of the present invention may also be recombinantly
produced. For example, cDNAs prepared by PCR amplification from
activated B-lymphocytes or hybridomas may be cloned into an
expression vector to form a cDNA library, which is then introduced
into a host cell for recombinant expression. The cDNA encoding a
specific desired protein may then be isolated from the library. The
isolated cDNA can be introduced into a suitable host cell for the
expression of the protein. Thus, recombinant techniques can be used
to produce specific native antibodies, hybrid antibodies capable of
simultaneous reaction with more than one antigen, chimeric
antibodies (e.g., the constant and variable regions are derived
from different sources), univalent antibodies that comprise one
heavy and light chain pair coupled with the Fc region of a third
(heavy) chain, Fab proteins, and the like. See U.S. Pat. No.
4,816,567; European Patent Publication No. 0088994; Munro, Nature,
312:597 (1984); Morrison, Science, 229:1202 (1985); Oi et al.,
BioTechniques, 4:214 (1986); and Wood et al., Nature, 314:446-449
(1985), all of which are incorporated herein by reference. Antibody
fragments such as Fv fragments, single-chain Fv fragments (scFv),
Fab' fragments, and F(ab').sub.2 fragments can also be
recombinantly produced by methods disclosed in, e.g., U.S. Pat. No.
4,946,778; Skerra & Pluckthun, Science, 240:1038-1041(1988);
Better et al., Science, 240:1041-1043 (1988); and Bird, et al.,
Science, 242:423-426 (1988), all of which are incorporated herein
by reference.
[0099] In a preferred embodiment, the antibodies provided in
accordance with the present invention are partially or fully
humanized antibodies. For this purpose, any methods known in the
art may be used. For example, partially humanized chimeric
antibodies having V regions derived from the tumor-specific mouse
monoclonal antibody, but human C regions are disclosed in Morrison
and Oi, Adv. Immunol., 44:65-92 (1989). In addition, fully
humanized antibodies can be made using transgenic non-human
animals. For example, transgenic non-human animals such as
transgenic mice can be produced in which endogenous immunoglobulin
genes are suppressed or deleted, while heterologous antibodies are
encoded entirely by exogenous immunoglobulin genes, preferably
human immunoglobulin genes, recombinantly introduced into the
genome. See e.g., U.S. Pat. Nos. 5,530,101; 5,545,806; 6,075,181;
PCT Publication No. WO 94/02602; Green et. al., Nat. Genetics, 7:
13-21 (1994); and Lonberg et al., Nature 368: 856-859 (1994), all
of which are incorporated herein by reference. The transgenic
non-human host animal may be immunized with suitable antigens such
as a protein complex of the present invention or one or more of the
interacting protein members thereof to illicit specific immune
response thus producing humanized antibodies. In addition, cell
lines producing specific humanized antibodies can also be derived
from the immunized transgenic non-human animals. For example,
mature B-lymphocytes obtained from a transgenic animal producing
humanized antibodies can be fused to myeloma cells and the
resulting hybridoma clones may be selected for specific humanized
antibodies with desired binding specificities. Alternatively, cDNAs
may be extracted from mature B-lymphocytes and used in establishing
a library that is subsequently screened for clones encoding
humanized antibodies with desired binding specificities.
[0100] In yet another embodiment, a bifunctional antibody is
provided that has two different antigen binding sites, each being
specific to a different interacting protein member in a protein
complex of the present invention. The bifunctional antibody may be
produced using a variety of methods known in the art. For example,
two different monoclonal antibody-producing hybridomas can be fused
together. One of the two hybridomas may produce a monoclonal
antibody specific against an interacting protein member of a
protein complex of the present invention, while the other hybridoma
generates a monoclonal antibody immunoreactive with another
interacting protein member of the protein complex. The thus formed
new hybridoma produces different antibodies including a desired
bifunctional antibody, i.e., an antibody immunoreactive with both
of the interacting protein members. The bifunctional antibody can
be readily purified. See Milstein and Cuello, Nature, 305:537-540
(1983).
[0101] Alternatively, a bifunctional antibody may also be produced
using heterobifunctional crosslinkers to chemically link two
different monoclonal antibodies, each being immunoreactive with a
different interacting protein member of a protein complex.
Therefore, the aggregate will bind to two interacting protein
members of the protein complex. See Staerz et al, Nature,
314:628-631(1985); Perez et al, Nature, 316:354-356 (1985).
[0102] In addition, bifunctional antibodies can also be produced by
recombinantly expressing light and heavy chain genes in a hybridoma
that itself produces a monoclonal antibody. As a result, a mixture
of antibodies including a bifunctional antibody is produced. See
DeMonte et al, Proc. Natl. Acad. Sci., USA, 87:2941-2945 (1990);
Lenz and Weidle, Gene, 87:213-218 (1990).
[0103] Preferably, a bifunctional antibody in accordance with the
present invention is produced by the method disclosed in U.S. Pat.
No. 5,582,996, which is incorporated herein by reference. For
example, two different Fabs can be provided and mixed together. The
first Fab can bind to an interacting protein member of a protein
complex, and has a heavy chain constant region having a first
complementary domain not naturally present in the Fab but capable
of binding a second complementary domain. The second Fab is capable
of binding another interacting protein member of the protein
complex, and has a heavy chain constant region comprising a second
complementary domain not naturally present in the Fab but capable
of binding to the first complementary domain. Each of the two
complementary domains is capable of stably binding to the other but
not to itself. For example, the leucine zipper regions of c-fos and
c-jun oncogenes may be used as the first and second complementary
domains. As a result, the first and second complementary domains
interact with each other to form a leucine zipper thus associating
the two different Fabs into a single antibody construct capable of
binding to two antigenic sites.
[0104] Other suitable methods known in the art for producing
bifunctional antibodies may also be used, which include those
disclosed in Holliger et al., Proc. Nat'l Acad. Sci. USA,
90:6444-6448 (1993); de Kruif et al., J. Biol. Chem., 271:7630-7634
(1996); Coloma and Morrison, Nat. Biotechnol., 15:159-163 (1997);
Muller et al., FEBS Lett., 422:259-264 (1998); and Muller et al.,
FEBS Lett., 432:45-49 (1998), all of which are incorporated herein
by reference.
4. Methods of Detecting Protein Complexes
[0105] Another aspect of the present invention relates to methods
for detecting the protein complexes of the present invention,
particularly for determining the concentration of a specific
protein complex in a patient sample.
[0106] In one embodiment, the concentration of a protein complex
having APOA1 and one or more proteins selected from the group
consisting of PRA1, GOLGIN-84, Syntaxin 2, APOB and FLJ20724 is
determined in cells, tissue, or an organ of a patient. For example,
the protein complex can be isolated or purified from a patient
sample obtained from cells, tissue, or an organ of the patient and
the amount thereof is determined. As described above, the protein
complex can be prepared from cells, tissue or organ samples by
coimmunoprecipitation using an antibody immunoreactive with an
interacting protein member, a bifunctional antibody that is
immunoreactive with two or more interacting protein members of the
protein complex, or preferably an antibody selectively
immunoreactive with the protein complex. When bifunctional
antibodies or antibodies immunoreactive with only free interacting
protein members are used, individual interacting protein members
not complexed with other proteins may also be isolated along with
the protein complex containing such individual proteins. However,
they can be readily separated from the protein complex using
methods known in the art, e.g., size-based separation methods such
as gel filtration, or by subtracting the protein complex from the
mixture using an antibody specific against another individual
interacting protein member. Additionally, proteins in a sample can
be separated in a gel such as polyacrylamide gel and subsequently
immunoblotted using an antibody immunoreactive with the protein
complex.
[0107] Alternatively, the concentration of the protein complex can
be determined in a sample without separation, isolation or
purification. For this purpose, it is preferred that an antibody
selectively immunoreactive with the specific protein complex is
used in an immunoassay. For example, immunocytochemical methods can
be used. Other well known antibody-based techniques can also be
used including, e.g., enzyme-linked immunosorbent assay (ELISA),
radioimmunoassay (RIA), immunoradiometric assays (IRMA),
fluorescent immunoassays, protein A immunoassays, and
immunoenzymatic assays (IEMA). See e.g., U.S. Pat. Nos. 4,376,110
and 4,486,530, both of which are incorporated herein by
reference.
[0108] In addition, since a specific protein complex is formed from
its interacting protein members, if one of the interacting protein
members is at a relatively low concentration in a patient, it may
be reasonably expected that the concentration of the protein
complex in the patient may also be low. Therefore, the
concentration of an individual interacting protein member of a
specific protein complex can be determined in a patient sample
which can then be used as a reasonably accurate indicator of the
concentration of the protein complex in the sample. For this
purpose, antibodies against an individual interacting protein
member of a specific complex can be used in any one of the methods
described above. In a preferred embodiment, the concentration of
each of the interacting protein members of a protein complex is
determined in a patient sample and the relative concentration of
the protein complex is then deduced.
[0109] In addition, the relative protein complex concentration in a
patient can also be determined by determining the concentration of
the mRNA encoding an interacting protein member of the protein
complex. Preferably, each interacting protein member's mRNA
concentration in a patient sample is determined. For this purpose,
methods for determining mRNA concentration generally known in the
art may all be used. Examples of such methods include, e.g.,
Northern blot assay, dot blot assay, PCR assay (preferably
quantitative PCR assay), in situ hybridization assay, and the
like.
[0110] As discussed above, the interactions between APOA1 and the
proteins PRA1, GOLGIN-84, Syntaxin 2, APOB and FLJ20724 suggest
that these proteins and/or the protein complexes formed by such
proteins may be involved in common biological processes and disease
pathways. In addition, the interactions between APOA1 and PRA1,
GOLGIN-84, Syntaxin 2, APOB and FLJ20724 under physiological
conditions may lead to the formation of protein complexes in vivo
that contain APOA1 and one or more of the APOA1-interacting
proteins. The protein complexes are expected to mediate the
functions and biological activities of APOA1 and PRA1, GOLGIN-84,
Syntaxin 2, APOB and FLJ20724. For example, APOA1 and the
APOA1-interacting proteins may be involved in cholesterol transport
and lipid metabolism and associated with diseases and disorders
such as dementia such as Alzheimer's disease and cardiovascular
diseases such as coronary heart disease, atherosclerosis,
hypercholesterolemia, Tangier disease and amyloidosis. Thus,
aberrations in the concentration and/or activity of the protein
complexes and/or the proteins such as APOA1 and the
APOA1-interacting proteins may result in diseases or disorders such
as dementia such as Alzheimer's disease and cardiovascular diseases
such as coronary heart disease, atherosclerosis,
hypercholesterolemia, Tangier disease and amyloidosis. Thus, the
aberration in the protein complexes or the individual proteins and
the degree of the aberration may be indicators for the diseases or
disorders. These aberrations may be used as parameters for
classifying and/or staging one of the above-described diseases. In
addition, they may also be indicators for patients' response to a
drug therapy.
[0111] Association between a physiological state (e.g.,
physiological disorder, predisposition to the disorder, a disease
state, response to a drug therapy, or other physiological phenomena
or phenotypes) and a specific aberration in a protein complex of
the present invention or an individual interacting member thereof
can be readily determined by comparative analysis of the protein
complex and/or the interacting members thereof in a normal
population and an abnormal or affected population. Thus, for
example, one can study the concentration, localization and
distribution of a particular protein complex, mutations in the
interacting protein members of the protein complex, and/or the
binding affinity between the interacting protein members in both a
normal population and a population affected with a particular
physiological disorder described above. The study results can be
compared and analyzed by statistical means. Any detected
statistically significant difference in the two populations would
indicate an association. For example, if the concentration of the
protein complex is statistically significantly higher in the
affected population than in the normal population, then it can be
reasonably concluded that higher concentration of the protein
complex is associated with the physiological disorder.
[0112] Thus, once an association is established between a
particular type of aberration in a particular protein complex of
the present invention or in an interacting protein member thereof
and a physiological disorder or disease or predisposition to the
physiological disorder or disease, then the particular
physiological disorder or disease or predisposition to the
physiological disorder or disease can be diagnosed or detected by
determining whether a patient has the particular aberration.
[0113] Accordingly, the present invention also provides a method
for diagnosing in a patient a disease or physiological disorder, or
a predisposition to the disease or disorder, such as dementia such
as Alzheimer's disease and cardiovascular diseases such as coronary
heart disease, atherosclerosis, hypercholesterolemia, Tangier
disease and amyloidosis by determining whether there is any
aberration in the patient with respect to a protein complex having
a first protein which is APOA1 interacting with a second protein
selected from the group consisting of PRA1, GOLGIN-84, Syntaxin 2,
APOB and FLJ20724. The same protein complex is analyzed in a normal
individual and is compared with the results obtained in the
patient. In this manner, any protein complex aberration in the
patient can be detected. As used herein, the term "aberration" when
used in the context of protein complexes of the present invention
means any alterations of a protein complex including increased or
decreased concentration of the protein complex in a particular cell
or tissue or organ or the total body, altered localization of the
protein complex in cellular compartments or in locations of a
tissue or organ, changes in binding affinity of an interacting
protein member of the protein complex, mutations in an interacting
protein member or the gene encoding the protein, and the like. As
will be apparent to a skilled artisan, the term "aberration" is
used in a relative sense. That is, an aberration is relative to a
normal condition.
[0114] As used herein, the term "diagnosis" means detecting a
disease or disorder or determining the stage or degree of a disease
or disorder. The term "diagnosis" also encompasses detecting a
predisposition to a disease or disorder, determining the
therapeutic effect of a drug therapy, or predicting the pattern of
response to a drug therapy or xenobiotics. The diagnosis methods of
the present invention may be used independently, or in combination
with other diagnosing and/or staging methods known in the medical
art for a particular disease or disorder.
[0115] Thus, in one embodiment, the method of diagnosis is
conducted by detecting, in a patient, the concentrations of one or
more protein complexes of the present invention using any one of
the methods described above, and determining whether the patient
has an aberrant concentration of the protein complexes.
[0116] The diagnosis may also be based on the determination of the
concentrations of one or more interacting protein members (at the
protein, cDNA or mRNA level) of a protein complex of the present
invention. An aberrant concentration of an interacting protein
member may indicate a physiological disorder or a predisposition to
a physiological disorder.
[0117] In another embodiment, the method of diagnosis comprises
determining, in a patient, the cellular localization, or tissue or
organ distribution of a protein complex of the present invention
and determining whether the patient has an aberrant localization or
distribution of the protein complex. For example,
immunocytochemical or immunohistochemical assays can be performed
on a cell, tissue or organ sample from a patient using an antibody
selectively immunoreactive with a protein complex of the present
invention. Antibodies immunoreactive with both an individual
interacting protein member and a protein complex containing the
protein member may also be used, in which case it is preferred that
antibodies immunoreactive with other interacting protein members
are also used in the assay. In addition, nucleic acid probes may
also be used in in situ hybridization assays to detect the
localization or distribution of the mRNAs encoding the interacting
protein members of a protein complex. Preferably, the mRNA encoding
each interacting protein member of a protein complex is detected
concurrently.
[0118] In yet another embodiment, the method of diagnosis of the
present invention comprises detecting any mutations in one or more
interacting protein members of a protein complex of the present
invention. In particular, it is desirable to determine whether the
interacting protein members have any mutations that will lead to,
or are associated with, changes in the functional activity of the
proteins or changes in their binding affinity to other interacting
protein members in forming a protein complex of the present
invention. Examples of such mutations include but are not limited
to, e.g., deletions, insertions and rearrangements in the genes
encoding the protein members, and nucleotide or amino acid
substitutions and the like. In a preferred embodiment, the domains
of the interacting protein members that are responsible for the
protein-protein interactions, and lead to protein complex
formation, are screened to detect any mutations therein. For
example, genomic DNA or cDNA encoding an interacting protein member
can be prepared from a patient sample, and sequenced. The thus
obtained sequence may be compared with known wild-type sequences to
identify any mutations. Alternatively, an interacting protein
member may be purified from a patient sample and analyzed by
protein sequencing or mass spectrometry to detect any amino acid
sequence changes. Any methods known in the art for detecting
mutations may be used, as will be apparent to skilled artisans
apprised of the present disclosure.
[0119] In another embodiment, the method of diagnosis includes
determining the binding constant of the interacting protein members
of one or more protein complexes. For example, the interacting
protein members can be obtained from a patient by direct
purification or by recombinant expression from genomic DNAs or
cDNAs prepared from a patient sample encoding the interacting
protein members. Binding constants represent the strength of the
protein-protein interaction between the interacting protein members
in a protein complex. Thus, by measuring binding constant, subtle
aberration in binding affinity may be detected.
[0120] A number of methods known in the art for estimating and
determining binding constants in protein-protein interactions are
reviewed in Phizicky and Fields, et al., Microbiol. Rev., 59:94-123
(1995), which is incorporated herein by reference. For example,
protein affinity chromatography may be used. First, columns are
prepared with different concentrations of an interacting protein
member which is covalently bound to the columns. Then a preparation
of an interacting protein partner is run through the column and
washed with buffer. The interacting protein partner bound to the
interacting protein member linked to the column is then eluted.
Binding constant is then estimated based on the concentrations of
the bound protein and the eluted protein. Alternatively, the method
of sedimentation through gradients monitors the rate of
sedimentation of a mixture of proteins through gradients of
glycerol or sucrose. At concentrations above the binding constant,
proteins can sediment as a protein complex. Thus, binding constant
can be calculated based on the concentrations. Other suitable
methods known in the art for estimating binding constant include
but are not limited to gel filtration column such as nonequilibrium
"small-zone" gel filtration columns (See e.g., Gill et al., J. Mol.
Biol., 220:307-324 (1991)), the Hummel-Dreyer method of equilibrium
gel filtration (See e.g., Hummel and Dreyer, Biochim. Biophys.
Acta, 63:530-532 (1962)) and large-zone equilibrium gel filtration
(See e.g., Gilbert and Kellett, J. Biol. Chem., 246:6079-6086
(1971)), sedimentation equilibrium (See e.g., Rivas and Minton,
Trends Biochem., 18:284-287 (1993)), fluorescence methods such as
fluorescence spectrum (See e.g., Otto-Bruc et al, Biochemistry,
32:8632-8645 (1993)) and fluorescence polarization or anisotropy
with tagged molecules (See e.g., Weiel and Hershey, Biochemistry,
20:5859-5865 (1981)), solution equilibrium measured with
immobilized binding protein (See e.g., Nelson and Long,
Biochemistry, 30:2384-2390 (1991)), and surface plasmon resonance
(See e.g., Panayotou et al., Mol. Cell. Biol., 13:3567-3576
(1993)).
[0121] In another embodiment, the diagnosis method of the present
invention comprises detecting protein-protein interactions in
functional assay systems such as the yeast two-hybrid system.
Accordingly, to determine the protein-protein interaction between
two interacting protein members that normally form a protein
complex in normal individuals, cDNAs encoding the interacting
protein members can be isolated from a patient to be diagnosed. The
thus cloned cDNAs or fragments thereof can be subcloned into
vectors for use in yeast two-hybrid system. Preferably a reverse
yeast two-hybrid system is used such that failure of interaction
between the proteins may be positively detected. The use of yeast
two-hybrid system or other systems for detecting protein-protein
interactions is known in the art and is described below in Section
5.3.1.
[0122] A kit may be used for conducting the diagnosis methods of
the present invention. Typically, the kit should contain, in a
carrier or compartmentalized container, reagents useful in any of
the above-described embodiments of the diagnosis method. The
carrier can be a container or support, in the form of, e.g., bag,
box, tube, rack, and is optionally compartmentalized. The carrier
may define an enclosed confinement for safety purposes during
shipment and storage. In one embodiment, the kit includes an
antibody selectively immunoreactive with a protein complex of the
present invention. In addition, antibodies against individual
interacting protein members of the protein complexes may also be
included. The antibodies may be labeled with a detectable marker
such as radioactive isotopes, or enzymatic or fluorescence markers.
Alternatively secondary antibodies such as labeled anti-IgG and the
like may be included for detection purposes. Optionally, the kit
can include one or more of the protein complexes of the present
invention prepared or purified from a normal individual or an
individual afflicted with a physiological disorder associated with
an aberration in the protein complexes or an interacting protein
member thereof. In addition, the kit may further include one or
more of the interacting protein members of the protein complexes of
the present invention prepared or purified from a normal individual
or an individual afflicted with a physiological disorder associated
with an aberration in the protein complexes or an interacting
protein member thereof. Suitable oligonucleotide primers useful in
the amplification of the genes or cDNAs for the interacting protein
members may also be provided in the kit. In particular, in a
preferred embodiment, the kit includes a first oligonucleotide
selectively hybridizable to the mRNA or cDNA encoding APOA1 and a
second oligonucleotide selectively hybridizable to the mRNA or cDNA
encoding a protein selected from the group consisting of PRA1,
GOLGIN-84, Syntaxin 2, APOB and FLJ20724. Additional
oligonucleotides hybridizing to a region of the gene encoding APOA1
and/or a region of the gene(s) encoding one or more APOA1
-interacting proteins, as identified in the present invention, may
also be included. Such oligonucleotides may be used as PCR primers
for, e.g., quantitative PCR amplification of mRNAs encoding APOA1
and an interacting partner thereof, or as hybridizing probes for
detecting the mRNAs. The oligonucleotides may have a length of from
about 8 nucleotides to about 100 nucleotides, preferably from about
12 to about 50 nucleotides, and more preferably from about 15 to
about 30 nucleotides. In addition, the kit may also contain
oligonucleotides that can be used as hybridization probes for
detecting the cDNAs or mRNAs encoding the interacting protein
members. Preferably, instructions for using the kit or reagents
contained therein are also included in the kit.
5. Use of Protein Complexes or Interacting Protein Members Thereof
in Screening Assays for Modulators
[0123] The protein complexes of the present invention and APOA1 and
APOA1-interacting proteins such as PRA1, GOLGIN-84, Syntaxin 2,
APOB and FLJ20724 can also be used in screening assays to identify
modulators of the protein complexes, APOA1, and/or the
APOA1-interacting proteins. In addition, homologues, derivatives
and fragments of APOA1 and homologues, derivatives and fragments of
the APOA1-interacting proteins may also be used in such screening
assays. As used herein, the term "modulator" encompasses any
compounds that can cause any forms of alteration of the biological
activities or functions of the proteins or protein complexes,
including, e.g., enhancing or reducing their biological activities,
increasing or decreasing their stability, altering their affinity
or specificity to certain other biological molecules, etc. In
addition, the term "modulator" as used herein also includes any
compounds that simply bind APOA1, APOA1-interacting proteins,
and/or the proteins complexes of the present invention. For
example, a modulator can be an "interaction antagonist" capable of
interfering with or disrupting or dissociating protein-protein
interaction between APOA1or a homologue, fragment or derivative
thereof and one or more proteins selected from the group consisting
of PRA1, GOLGIN-84, Syntaxin 2, APOB and FLJ20724 or a homologue,
fragment or derivative thereof. A modulator can also be an
"interaction agonist" that initiates or strengthens the interaction
between the protein members of a protein complex of the present
invention, or homologues, fragments or derivatives thereof.
[0124] Accordingly, the present invention provides screening
methods for selecting modulators of APOA1, or a mutant form
thereof, an APOA1-interacting protein selected from the group
consisting of PRA1, GOLGIN-84, Syntaxin 2, APOB and FLJ20724, or a
mutant form thereof, or a protein complex formed between APOA1, or
a mutant form thereof, and one or more of the APOA1 -interacting
proteins, or a mutant forms thereof. Screening methods are also
provided for selecting modulators of APOA1 homologues, derivatives
or fragments, or homologues, derivatives or fragments of an
APOA1-interacting protein, or a protein complex formed between an
APOA1 homologue, derivative or fragment and a homologue or
derivative or fragment of an APOA1-interacting protein, or
proteins.
[0125] The selected compounds can be tested for their ability to
modulate (interfere with or strengthen) the interaction between the
interacting partners within the protein complexes of the present
invention. In addition, the compounds can also be further tested
for their ability to modulate (inhibit or enhance) cellular
functions such as cholesterol transport and lipid metabolism in
cells as well as their effectiveness in treating diseases such as
Alzheimer's disease and cardiovascular disease.
[0126] The modulators selected in accordance with the screening
methods of the present invention can be effective in modulating the
functions or activities of APOA1, an APOA1-interacting protein, or
the protein complexes of the present invention. For example,
compounds capable of binding to the protein complexes may be
capable of modulating the functions of the protein complexes.
Additionally, compounds that interfere with, weaken, dissociate or
disrupt, or alternatively, initiate, facilitate or stabilize the
protein-protein interaction between the interacting protein members
of the protein complexes can also be effective in modulating the
functions or activities of the protein complexes. Thus, the
compounds identified in the screening methods of the present
invention can be made into therapeutically or prophylactically
effective drugs for preventing or ameliorating diseases, disorders
or symptoms caused by or associated with aberrations in the protein
complexes or APOA1 or the APOA1-interacting proteins of the present
invention. Alternatively, they may be used as leads to aid the
design and identification of therapeutically or prophylactically
effective compounds for diseases, disorders or symptoms caused by
or associated with aberrations in the protein complexes or APOA1 or
the APOA1-interacting proteins of the present invention. The
protein complexes and/or interacting protein members thereof in
accordance with the present invention can be used in any of a
variety of drug screening techniques. Drug screening can be
performed as described herein or using well-known techniques, such
as those described in U.S. Pat. Nos. 5,800,998 and 5,891,628, both
of which are incorporated herein by reference.
5.1. Test Compounds
[0127] Any test compounds may be screened in the screening assays
of the present invention to select modulators of APOA1, an
APOA1-containing protein complex and/or an APOA1-interacting
protein of the present invention. By the term "selecting" or
"select" compounds it is intended to encompass both (a) choosing
compounds from a group previously unknown to be modulators of
APOA1, an APOA1-containing protein complex and/or an
APOA1-interacting protein of the present invention, and (b) testing
compounds that are known to be capable of binding, or modulating
the functions and activities of, APOA1, an APOA1-containing protein
complex and/or an APOA1-interacting protein of the present
invention. Both types of compounds are generally referred to herein
as "test compounds." The test compounds may include, by way of
example, proteins (e.g., antibodies, small peptides, artificial or
natural proteins), nucleic acids, and derivatives, mimetics and
analogs thereof, and small organic molecules having a molecular
weight of no greater than 10,000 daltons, more preferably less than
5,000 daltons. Preferably, the test compounds are provided in
library formats known in the art, e.g., in chemically synthesized
libraries, recombinantly expressed libraries (e.g., phage display
libraries), and in vitro translation-based libraries (e.g.,
ribosome display libraries).
[0128] For example, the screening assays of the present invention
can be used in the antibody production processes described in
Section 3 to select antibodies with desirable specificities.
Various forms antibodies or derivatives thereof may be screened,
including but not limited to, polyclonal antibodies, monoclonal
antibodies, bifunctional antibodies, chimeric antibodies, single
chain antibodies, antibody fragments such as Fv fragments,
single-chain Fv fragments (scFv), Fab' fragments, and F(ab').sub.2
fragments, and various modified forms of antibodies such as
catalytic antibodies, and antibodies conjugated to toxins or drugs,
and the like. The antibodies can be of any types such as IgG, IgE,
IgA, or IgM. Humanized antibodies are particularly preferred.
Preferably, the various antibodies and antibody fragments may be
provided in libraries to allow large-scale high throughput
screening. For example, expression libraries expressing antibodies
or antibody fragments may be constructed by a method disclosed,
e.g., in Huse et al., Science, 246:1275-1281 (1989), which is
incorporated herein by reference. Single-chain Fv (scFv) antibodies
are of particular interest in diagnostic and therapeutic
applications. Methods for providing antibody libraries are also
provided in U.S. Pat. Nos. 6,096,551; 5,844,093; 5,837,460;
5,789,208; and 5,667,988, all of which are incorporated herein by
reference.
[0129] Peptidic test compounds may be peptides having L-amino acids
and/or D-amino acids, phosphopeptides, and other types of peptides.
The screened peptides can be of any size, but preferably have less
than about 50 amino acids. Smaller peptides are easier to deliver
into a patient's body. Various forms of modified peptides may also
be screened. Like antibodies, peptides can also be provided in,
e.g., combinatorial libraries. See generally, Gallop et al., J.
Med. Chem., 37:1233-1251 (1994). Methods for making random peptide
libraries are disclosed in, e.g., Devlin et al., Science,
249:404-406 (1990). Other suitable methods for constructing peptide
libraries and screening peptides therefrom are disclosed in, e.g.,
Scott and Smith, Science, 249:386-390 (1990); Moran et al., J. Am.
Chem. Soc., 117:10787-10788 (1995) (a library of electronically
tagged synthetic peptides); Stachelhaus et al., Science, 269:69-72
(1995); U.S. Pat. Nos. 6,156,511; 6,107,059; 6,015,561; 5,750,344;
5,834,318; 5,750,344, all of which are incorporated herein by
reference. For example, random-sequence peptide phage display
libraries may be generated by cloning synthetic oligonucleotides
into the gene III or gene VIII of an E. coli. filamentous phage.
The thus generated phage can propagate in E. coli. and express
peptides encoded by the oligonucleotides as fusion proteins on the
surface of the phage. Scott and Smith, Science, 249:368-390 (1990).
Alternatively, the "peptides on plasmids" method may also be used
to form peptide libraries. In this method, random peptides may be
fused to the C-terminus of the E. coli. Lac repressor by
recombinant technologies and expressed from a plasmid that also
contains Lac repressor-binding sites. As a result, the peptide
fusions bind to the same plasmid that encodes them.
[0130] Small organic or inorganic non-peptide non-nucleotide
compounds are preferred test compounds for the screening assays of
the present invention. They too can be provided in a library
format. See generally, Gordan et al. J. Med. Chem., 37:1385-1401
(1994). For example, benzodiazepine libraries are provided in Bunin
and Ellman, J. Am. Chem. Soc., 114:10997-10998 (1992), which is
incorporated herein by reference. A method for constructing and
screening peptoid libraries are disclosed in Simon et al., Proc.
Natl. Acad. Sci. USA, 89:9367-9371 (1992). Methods for the
biosynthesis of novel polyketides in a library format are described
in McDaniel et al, Science, 262:1546-1550 (1993) and Kao et al.,
Science, 265:509-512 (1994). Various libraries of small organic
molecules and methods of construction thereof are disclosed in U.S.
Pat. No. 6,162,926 (multiply-substituted fullerene derivatives);
U.S. Pat. No. 6,093,798 (hydroxamic acid derivatives); U.S. Pat.
No. 5,962,337 (combinatorial 1,4-benzodiazepin-2,5-dione library);
U.S. Pat. No. 5,877,278 (Synthesis of N-substituted oligomers);
U.S. Pat. No. 5,866,341 (compositions and methods for screening
drug libraries); U.S. Pat. No. 5,792,821 (polymerizable
cyclodextrin derivatives); U.S. Pat. No. 5,766,963
(hydroxypropylamine library); and U.S. Pat. No. 5,698,685
(morpholino-subunit combinatorial library), all of which are
incorporated herein by reference.
[0131] Other compounds such as oligonucleotides and peptide nucleic
acids (PNA), and analogs and derivatives thereof may also be
screened to identify clinically useful compounds. Combinatorial
libraries of oligonucleotides are also known in the art. See Gold
et al., J. Biol. Chem., 270:13581-13584 (1995).
5.2. In vitro Screening Assays
[0132] The test compounds may be screened in an in vitro assay to
identify compounds capable of binding the protein complexes or
interacting protein members thereof in accordance with the present
invention. For this purpose, a test compound is contacted with a
protein complex or an interacting protein member thereof under
conditions and for a time sufficient to allow specific interaction
between the test compound and the target components to occur and
thus binding of the compound to the target forming a complex.
Subsequently, the binding event is detected.
[0133] Various screening techniques known in the art may be used in
the present invention. The protein complexes and the interacting
protein members thereof may be prepared by any suitable methods,
e.g., by recombinant expression and purification. The protein
complexes and/or interacting protein members thereof (both are
referred to as "target" hereinafter in this section) may be free in
solution. A test compound may be mixed with a target forming a
liquid mixture. The compound may be labeled with a detectable
marker. Upon mixing under suitable conditions, the binding complex
having the compound and the target may be co-immunoprecipitated and
washed. The compound in the precipitated complex may be detected
based on the marker on the compound.
[0134] In a preferred embodiment, the target is immobilized on a
solid support or on a cell surface. Preferably, the target can be
arrayed into a protein microchip in a method described in Section
2.3. For example, a target may be immobilized directly onto a
microchip substrate such as glass slides or onto a multi-well
plates using non-neutralizing antibodies, i.e., antibodies capable
of binding to the target but do not substantially affect its
biological activities. To affect the screening, test compounds can
be contacted with the immobilized target to allow binding to occur
to form complexes under standard binding assay conditions. Either
the targets or test compounds are labeled with a detectable marker
using well-known labeling techniques. For example, U.S. Pat. No.
5,741,713 discloses combinatorial libraries of biochemical
compounds labeled with NMR active isotopes. To identify binding
compounds, one may measure the formation of the target-test
compound complexes or kinetics for the formation thereof. When
combinatorial libraries of organic non-peptide non-nucleic acid
compound are screened, it is preferred that labeled or encoded (or
"tagged") combinatorial libraries are used to allow rapid decoding
of lead structures. This is especially important because, unlike
biological libraries, individual compounds found in chemical
libraries cannot be amplified by self-amplification. Tagged
combinatorial libraries are provided in, e.g., Borchardt and Still,
J. Am. Chem. Soc., 116:373-374 (1994) and Moran et al., J. Am.
Chem. Soc., 117:10787-10788 (1995), both of which are incorporated
herein by reference.
[0135] Alternatively, the test compounds can be immobilized on a
solid support, e.g., forming a microarray of test compounds. The
target protein or protein complex is then contacted with the test
compounds. The target may be labeled with any suitable detection
marker. For example, the target may be labeled with radioactive
isotopes or fluorescence marker before binding reaction occurs.
Alternatively, after the binding reactions, antibodies that are
immunoreactive with the target and are labeled with radioactive
materials, fluorescence markers, enzymes, or labeled secondary
anti-Ig antibodies may be used to detect any bound target thus
identifying the binding compound. One example of this embodiment is
the protein probing method. That is, the target provided in
accordance with the present invention is used as a probe to screen
expression libraries of proteins or random peptides. The expression
libraries can be phage display libraries, in vitro
translation-based libraries, or ordinary expression cDNA libraries.
The libraries may be immobilized on a solid support such as
nitrocellulose filters. See e.g., Sikela and Hahn, Proc. Natl.
Acad. Sci. USA, 84:3038-3042 (1987). The probe may be labeled with
a radioactive isotope or a fluorescence marker. Alternatively, the
probe can be biotinylated and detected with a streptavidin-alkaline
phosphatase conjugate. More conveniently, the bound probe may be
detected with an antibody.
[0136] In yet another embodiment, a known ligand capable of binding
to the target can be used in competitive binding assays. Complexes
between the known ligand and the target can be formed and then
contacted with test compounds. The ability of a test compound to
interfere with the interaction between the target and the known
ligand is measured. One exemplary ligand is an antibody capable of
specifically binding the target. Particularly, such an antibody is
especially useful for identifying peptides that share one or more
antigenic determinants of the target protein complex or interacting
protein members thereof.
[0137] In a specific embodiment, a protein complex used in the
screening assay includes a hybrid protein as described in Section
2.1, which is formed by fusion of two interacting protein members
or fragments or interaction domains thereof. The hybrid protein may
also be designed such that it contains a detectable epitope tag
fused thereto. Suitable examples of such epitope tags include
sequences derived from, e.g., influenza virus hemagglutinin (HA),
Simian Virus 5 (V5), polyhistidine (6xHis), c-myc, lacZ, GST, and
the like.
[0138] Test compounds may be also screened in an in vitro assay to
identify compounds capable of dissociating the protein complexes
identified in accordance with the present invention. Thus, for
example, an APOA1-containing protein complex can be contacted with
a test compound and the protein complex can be detected.
Conversely, test compounds may also be screened to identify
compounds capable of enhancing the interaction between APOA1 and an
APOA1 -interacting protein or stabilizing the protein complex
formed by the two or more proteins.
[0139] The assay can be conducted in similar manners as the binding
assays described above. For example, the presence or absence of a
particular protein complex can be detected by an antibody
selectively immunoreactive with the protein complex. Thus, after
incubation of the protein complex with a test compound, an
immunoprecipitation assay can be conducted with the antibody. If
the test compound disrupts the protein complex, then the amount of
immunoprecipitated protein complex in this assay will be
significantly less than that in a control assay in which the same
protein complex is not contacted with the test compound. Similarly,
two proteins the interaction between which is to be enhanced may be
incubated together with a test compound. Thereafter, a protein
complex may be detected by the selectively immunoreactive antibody.
The amount of protein complex may be compared to that formed in the
absence of the test compound. Various other detection methods may
be suitable in the dissociation assay, as will be apparent to
skilled artisan apprised of the present disclosure.
5.3. In vivo Screening Assays
[0140] Test compounds can also be screened in any in vivo assays to
select modulators of the protein complexes or interacting protein
members thereof in accordance with the present invention. For
example, any in vivo assays known in the art to be useful in
identifying compounds capable of strengthening or interfering with
the stability of the protein complexes of the present invention may
be used.
5.3.1. Two-Hybrid Assays
[0141] In a preferred embodiment, one of the yeast two-hybrid
systems or their analogous or derivative forms is used. Examples of
suitable two-hybrid systems known in the art include, but are not
limited to, those disclosed in U.S. Pat. Nos. 5,283,173; 5,525,490;
5,585,245; 5,637,463; 5,695,941; 5,733,726; 5,776,689; 5,885,779;
5,905,025; 6,037,136; 6,057,101; 6,114,111; and Bartel and Fields,
eds., The Yeast Two-Hybrid System, Oxford University Press, New
York, N.Y., 1997, all of which are incorporated herein by
reference.
[0142] Typically, in a classic transcription-based two-hybrid
assay, two chimeric genes are prepared encoding two fusion
proteins: one contains a transcription activation domain fused to
an interacting protein member of a protein complex of the present
invention or an interaction domain or fragment of the interacting
protein member, while the other fusion protein includes a DNA
binding domain fused to another interacting protein member of the
protein complex or a fragment or interaction domain thereof. For
the purpose of convenience, the two interacting protein members,
fragments or interaction domains thereof are referred to as "bait
fusion protein" and "prey fusion protein," respectively. The
chimeric genes encoding the fusion proteins are termed "bait
chimeric gene" and "prey chimeric gene," respectively. Typically, a
"bait vector" and a "prey vector" are provided for the expression
of a bait chimeric gene and a prey chimeric gene, respectively.
5.3.1.1. Vectors
[0143] Many types of vectors can be used in a transcription-based
two-hybrid assay. Methods for the construction of bait vectors and
prey vectors should be apparent to skilled artisans in the art
apprised of the present disclosure. See generally, Current
Protocols in Molecular Biology, Vol. 2, Ed. Ausubel, et al., Greene
Publish. Assoc. & Wiley Interscience, Ch. 13, 1988; Glover, DNA
Cloning, Vol. II, IRL Press, Wash., D.C., Ch. 3, 1986; Bitter, et
al., in Methods in Enzymology 153:516-544 (1987); The Molecular
Biology of the Yeast Saccharomyces, Eds. Strathern et al., Cold
Spring Harbor Press, Vols. I and II, 1982; and Rothstein in DNA
Cloning: A Practical Approach, Vol. 11, Ed. DM Glover, IRL Press,
Wash., D.C., 1986.
[0144] Generally, the bait and prey vectors include an expression
cassette having a promoter operably linked to a chimeric gene for
the transcription of the chimeric gene. The vectors may also
include an origin of DNA replication for the replication of the
vectors in host cells and a replication origin for the
amplification of the vectors in, e.g., E. coli, and selection
marker(s) for selecting and maintaining only those host cells
harboring the vectors. Additionally, the expression cassette
preferably also contains inducible elements, which function to
control the expression of a chimeric gene. Making the expression of
the chimeric genes inducible and controllable is especially
important in the event that the fusion proteins or components
thereof are toxic to the host cells. Other regulatory sequences
such as transcriptional enhancer sequences and translation
regulation sequences (e.g., Shine-Dalgarno sequence) can also be
included in the expression cassette. Termination sequences such as
the bovine growth hormone, SV40, lacZ and AcMNPV polyhedral
polyadenylation signals may also be operably linked to a chimeric
gene in the expression cassette. An epitope tag coding sequence for
detection and/or purification of the fusion proteins can also be
operably linked to the chimeric gene in the expression cassette.
Examples of useful epitope tags include, but are not limited to,
influenza virus hemagglutinin (HA), Simian Virus 5 (V5),
polyhistidine (6xHis), c-myc, lacZ, GST, and the like. Proteins
with polyhistidine tags can be easily detected and/or purified with
Ni affinity columns, while specific antibodies to many epitope tags
are generally commercially available. The vectors can be introduced
into the host cells by any techniques known in the art, e.g., by
direct DNA transformation, microinjection, electroporation, viral
infection, lipofection, gene gun, and the like. The bait and prey
vectors can be maintained in host cells in an extrachromosomal
state, i.e., as self-replicating plasmids or viruses.
Alternatively, one or both vectors can be integrated into
chromosomes of the host cells by conventional techniques such as
selection of stable cell lines or site-specific recombination.
[0145] The in vivo assays of the present invention can be conducted
in many different host cells, including but not limited to
bacteria, yeast cells, plant cells, insect cells, and mammalian
cells. A skilled artisan will recognize that the designs of the
vectors can vary with the host cells used. In one embodiment, the
assay is conducted in prokaryotic cells such as Escherichia coli,
Salmonella, Klebsiella, Pseudomonas, Caulobacter, and Rhizobium.
Suitable origins of replication for the expression vectors useful
in this embodiment of the present invention include, e.g., the
ColE1, pSC101, and M13 origins of replication. Examples of suitable
promoters include, for example, the T7 promoter, the lacZ promoter,
and the like. In addition, inducible promoters are also useful in
modulating the expression of the chimeric genes. For example, the
lac operon from bacteriophage lambda plac5 is well known in the art
and is inducible by the addition of IPTG to the growth medium.
Other known inducible promoters useful in a bacteria expression
system include pL of bacteriophage .lambda., the trp promoter, and
hybrid promoters such as the tac promoter, and the like.
[0146] In addition, selection marker sequences for selecting and
maintaining only those prokaryotic cells expressing the desirable
fusion proteins should also be incorporated into the expression
vectors. Numerous selection markers including auxotrophic markers
and antibiotic resistance markers are known in the art and can all
be useful for purposes of this invention. For example, the bla
gene, which confers ampicillin resistance, is the most commonly
used selection marker in prokaryotic expression vectors. Other
suitable markers include genes that confer neomycin, kanamycin, or
hygromycin resistance to the host cells. In fact, many vectors are
commercially available from vendors such as Invitrogen Corp. of
Carlsbad, Calif., Clontech Corp. of Palo Alto, Calif., and
Stratagene Corp. of La Jolla, Calif., and Promega Corp. of Madison,
Wis. These commercially available vectors, e.g., pBR322, pSPORT,
pBluescriptIISK, pcDNAI, and pcDNAII all have a multiple cloning
site into which the chimeric genes of the present invention can be
conveniently inserted using conventional recombinant techniques.
The constructed expression vectors can be introduced into host
cells by various transformation or transfection techniques
generally known in the art.
[0147] In another embodiment, mammalian cells are used as host
cells for the expression of the fusion proteins and detection of
protein-protein interactions. For this purpose, virtually any
mammalian cells can be used including normal tissue cells, stable
cell lines, and transformed tumor cells. Conveniently, mammalian
cell lines such as CHO cells, Jurkat T cells, NIH 3T3 cells,
HEK-293 cells, CV-1 cells, COS-1 cells, HeLa cells, VERO cells,
MDCK cells, WI38 cells, and the like are used. Mammalian expression
vectors are well known in the art and many are commercially
available. Examples of suitable promoters for the transcription of
the chimeric genes in mammalian cells include viral transcription
promoters derived from adenovirus, simian virus 40 (SV40) (e.g.,
the early and late promoters of SV40), Rous sarcoma virus (RSV),
and cytomegalovirus (CMV) (e.g., CMV immediate-early promoter),
human immunodeficiency virus (HIV) (e.g., long terminal repeat
(LTR)), vaccinia virus (e.g., 7.5K promoter), and herpes simplex
virus (HSV) (e.g., thymidine kinase promoter). Inducible promoters
can also be used. Suitable inducible promoters include, for
example, the tetracycline responsive element (TRE) (See Gossen et
al., Proc. Natl. Acad. Sci. USA, 89:5547-5551 (1992)),
metallothionein IIA promoter, ecdysone-responsive promoter, and
heat shock promoters. Suitable origins of replication for the
replication and maintenance of the expression vectors in mammalian
cells include, e.g., the Epstein Barr origin of replication in the
presence of the Epstein Barr nuclear antigen (see Sugden et al.,
Mole. Cell. Biol., 5:410-413 (1985)) and the SV40 origin of
replication in the presence of the SV40 T antigen (which is present
in COS-1 and COS-7 cells) (see Margolskee et al., Mole. Cell.
Biol., 8:2837 (1988)). Suitable selection markers include, but are
not limited to, genes conferring resistance to neomycin,
hygromycin, zeocin, and the like. Many commercially available
mammalian expression vectors may be useful for the present
invention, including, e.g., pCEP4, pcDNAI, pIND, pSecTag2, pVAX1,
pcDNA3.1, and pBI-EGFP, and pDisplay. The vectors can be introduced
into mammalian cells using any known techniques such as calcium
phosphate precipitation, lipofection, electroporation, and the
like. The bait vector and prey vector can be co-transformed into
the same cell or, alternatively, introduced into two different
cells which are subsequently fused together by cell fusion or other
suitable techniques.
[0148] Viral expression vectors, which permit introduction of
recombinant genes into cells by viral infection, can also be used
for the expression of the fusion proteins. Viral expression vectors
generally known in the art include viral vectors based on
adenovirus, bovine papilloma virus, murine stem cell virus (MSCV),
MFG virus, and retrovirus. See Sarver, et al., Mol. Cell. Biol., 1:
486 (1981); Logan & Shenk, Proc. Natl. Acad. Sci. USA,
81:3655-3659 (1984); Mackett, et al., Proc. Natl. Acad. Sci. USA,
79:7415-7419 (1982); Mackett, et al., J. Virol., 49:857-864 (1984);
Panicali, et al., Proc. Natl. Acad. Sci. USA, 79:4927-4931 (1982);
Cone & Mulligan, Proc. Natl. Acad. Sci. USA, 81:6349-6353
(1984); Mann et al., Cell, 33:153-159 (1993); Pear et al., Proc.
Natl. Acad. Sci. USA, 90:8392-8396 (1993); Kitamura et al., Proc.
Natl. Acad. Sci. USA, 92:9146-9150 (1995); Kinsella et al., Human
Gene Therapy, 7:1405-1413 (1996); Hofmann et al., Proc. Natl. Acad.
Sci. USA, 93:5185-5190 (1996); Choate et al., Human Gene Therapy,
7:2247 (1996); WO 94/19478; Hawley et al., Gene Therapy, 1:136
(1994) and Rivere et al., Genetics, 92:6733 (1995), all of which
are incorporated by reference.
[0149] Generally, to construct a viral vector, a chimeric gene
according to the present invention can be operably linked to a
suitable promoter. The promoter-chimeric gene construct is then
inserted into a non-essential region of the viral vector, typically
a modified viral genome. This results in a viable recombinant virus
capable of expressing the fusion protein encoded by the chimeric
gene in infected host cells. Once in the host cell, the recombinant
virus typically is integrated into the genome of the host cell.
However, recombinant bovine papilloma viruses typically replicate
and remain as extrachromosomal elements.
[0150] In another embodiment, the detection assays of the present
invention are conducted in plant cell systems. Methods for
expressing exogenous proteins in plant cells are well known in the
art. See generally, Weissbach & Weissbach, Methods for Plant
Molecular Biology, Academic Press, NY, 1988; Grierson & Corey,
Plant Molecular Biology, 2d Ed., Blackie, London, 1988. Recombinant
virus expression vectors based on, e.g., cauliflower mosaic virus
(CaMV) or tobacco mosaic virus (TMV) can all be used.
Alternatively, recombinant plasmid expression vectors such as Ti
plasmid vectors and Ri plasmid vectors are also useful. The
chimeric genes encoding the fusion proteins of the present
invention can be conveniently cloned into the expression vectors
and placed under control of a viral promoter such as the 35S RNA
and 19S RNA promoters of CaMV or the coat protein promoter of TMV,
or of a plant promoter, e.g., the promoter of the small subunit of
RUBISCO and heat shock promoters (e.g., soybean hsp17.5-E or
hsp17.3-B promoters).
[0151] In addition, the in vivo assay of the present invention can
also be conducted in insect cells, e.g., Spodoptera frugiperda
cells, using a baculovirus expression system. Expression vectors
and host cells useful in this system are well known in the art and
are generally available from various commercial vendors. For
example, the chimeric genes of the present invention can be
conveniently cloned into a non-essential region (e.g., the
polyhedrin gene) of an Autographa californica nuclear polyhedrosis
virus (AcNPV) vector and placed under control of an AcNPV promoter
(e.g., the polyhedrin promoter). The non-occluded recombinant
viruses thus generated can be used to infect host cells such as
Spodoptera frugiperda cells in which the chimeric genes are
expressed. See U.S. Pat. No. 4,215,051.
[0152] In a preferred embodiment of the present invention, the
fusion proteins are expressed in a yeast expression system using
yeasts such as Saccharomyces cerevisiae, Hansenula polymorpha,
Pichia pastoris, and Schizosaccharomyces pombe as host cells. The
expression of recombinant proteins in yeasts is a well-developed
field, and the techniques useful in this respect are disclosed in
detail in The Molecular Biology of the Yeast Saccharomyces, Eds.
Strathern et al., Vols. I and II, Cold Spring Harbor Press, 1982;
Ausubel et al., Current Protocols in Molecular Biology, New York,
Wiley, 1994; and Guthrie and Fink, Guide to Yeast Genetics and
Molecular Biology, in Methods in Enzymology, Vol. 194, 1991, all of
which are incorporated herein by reference. Sudbery, Curr. Opin.
Biotech., 7:517-524 (1996) reviews the success in the art in
expressing recombinant proteins in various yeast species; the
entire content and references cited therein are incorporated herein
by reference. In addition, Bartel and Fields, eds., The Yeast
Two-Hybrid System, Oxford University Press, New York, N.Y., 1997
contains extensive discussions of recombinant expression of fusion
proteins in yeasts in the context of various yeast two-hybrid
systems, and cites numerous relevant references. These and other
methods known in the art can all be used for purposes of the
present invention. The application of such methods to the present
invention should be apparent to a skilled artisan apprised of the
present disclosure.
[0153] Generally, each of the two chimeric genes is included in a
separate expression vector (bait vector and prey vector). Both
vectors can be co-transformed into a single yeast host cell. As
will be apparent to a skilled artisan, it is also possible to
express both chimeric genes from a single vector. In a preferred
embodiment, the bait vector and prey vector are introduced into two
haploid yeast cells of opposite mating types, e.g., a-type and
.alpha.-type, respectively. The two haploid cells can be mated at a
desired time to form a diploid cell expressing both chimeric
genes.
[0154] Generally, the bait and prey vectors for recombinant
expression in yeast include a yeast replication origin such as the
2.mu. origin or the ARSH4 sequence for the replication and
maintenance of the vectors in yeast cells. Preferably, the vectors
also have a bacteria origin of replication (e.g., ColE1) and a
bacteria selection marker (e.g., amp.sup.R marker, i.e., bla gene).
Optionally, the CEN6 centromeric sequence is included to control
the replication of the vectors in yeast cells. Any constitutive or
inducible promoters capable of driving gene transcription in yeast
cells may be employed to control the expression of the chimeric
genes. Such promoters are operably linked to the chimeric genes.
Examples of suitable constitutive promoters include but are not
limited to the yeast ADH1, PGK1 , TEF2, GPD1, HIS3, and CYC1
promoters. Example of suitable inducible promoters include but are
not limited to the yeast GAL1 (inducible by galactose), CUP1
(inducible by Cu.sup.++), and FUS1 (inducible by pheromone)
promoters; the AOX/MOX promoter from H. polymorpha and P. Pastoris
(repressed by glucose or ethanol and induced by methanol); chimeric
promoters such as those that contain LexA operators (inducible by
LexA-containing transcription factors); and the like. Inducible
promoters are preferred when the fusion proteins encoded by the
chimeric genes are toxic to the host cells. If it is desirable,
certain transcription repressing sequences such as the upstream
repressing sequence (URS) from SPO13 promoter can be operably
linked to the promoter sequence, e.g., to the 5' end of the
promoter region. Such upstream repressing sequences function to
fine-tune the expression level of the chimeric genes.
[0155] Preferably, a transcriptional termination signal is operably
linked to the chimeric genes in the vectors. Generally,
transcriptional termination signal sequences derived from, e.g.,
the CYC1 and ADH1 genes can be used.
[0156] Additionally, it is preferred that the bait vector and prey
vector contain one or more selectable markers for the selection and
maintenance of only those yeast cells that harbor one or both
chimeric genes. Any selectable markers known in the art can be used
for purposes of this invention so long as yeast cells expressing
the chimeric gene(s) can be positively identified or negatively
selected. Examples of markers that can be positively identified are
those based on color assays, including the lacZ gene (which encodes
.beta.-galactosidase), the firefly luciferase gene, secreted
alkaline phosphatase, horseradish peroxidase, the blue fluorescent
protein (BFP), and the green fluorescent protein (GFP) gene (see
Cubitt et al., Trends Biochem. Sci., 20:448-455 (1995)). Other
markers allowing detection by fluorescence, chemiluminescence, UV
absorption, infrared radiation, and the like can also be used.
Among the markers that can be selected are auxotrophic markers
including, but not limited to, URA3, HIS3, TRP1, LEU2, LYS2, ADE2,
and the like. Typically, for purposes of auxotrophic selection, the
yeast host cells transformed with bait vector and/or prey vector
are cultured in a medium lacking a particular nutrient. Other
selectable markers are not based on auxotrophies, but rather on
resistance or sensitivity to an antibiotic or other xenobiotic.
Examples of such markers include but are not limited to
chloramphenicol acetyl transferase (CAT) gene, which confers
resistance to chloramphenicol; CAN1 gene, which encodes an arginine
permease and thereby renders cells sensitive to canavanine (see
Sikorski et al., Meth. Enzymol., 194:302-318 (1991)); the bacterial
kanamycin resistance gene (kan.sup.R), which renders eukaryotic
cells resistant to the aminoglycoside G418 (see Wach et al., Yeast,
10:1793-1808 (1994)); and CYH2 gene, which confers sensitivity to
cycloheximide (see Sikorski et al., Meth. Enzymol., 194:302-318
(1991)). In addition, the CUP1 gene, which encodes metallothionein
and thereby confers resistance to copper, is also a suitable
selection marker. Each of the above selection markers may be used
alone or in combination. One or more selection markers can be
included in a particular bait or prey vector. The bait vector and
prey vector may have the same or different selection markers. In
addition, the selection pressure can be placed on the transformed
host cells either before or after mating the haploid yeast
cells.
[0157] As will be apparent, the selection markers used should
complement the host strains in which the bait and/or prey vectors
are expressed. In other words, when a gene is used as a selection
marker gene, a yeast strain lacking the selection marker gene (or
having mutation in the corresponding gene) should be used as host
cells. Numerous yeast strains or derivative strains corresponding
to various selection markers are known in the art. Many of them
have been developed specifically for certain yeast two-hybrid
systems. The application and optional modification of such strains
with respect to the present invention should be apparent to a
skilled artisan apprised of the present disclosure. Methods for
genetically manipulating yeast strains using genetic crossing or
recombinant mutagenesis are well known in the art. See e.g.,
Rothstein, Meth. Enzymol., 101:202-211 (1983). By way of example,
the following yeast strains are well known in the art, and can be
used in the present invention upon necessary modifications and
adjustment:
[0158] L40 strain which has the genotype MAT.alpha. his3.DELTA.200
trp1-901 leu2-3,112 ade2 LYS2::(lexAop)4-HIS3
URA3::(lexAop)8-lacZ;
[0159] EGY48 strain which has the genotype MAT.alpha. trp1 his3
ura36ops-LEU2; and
[0160] MaV103 strain which has the genotype MAT.alpha.ura3-52
leu2-3,112 trp1-901 his3.DELTA.200 ade2-101 gal4.DELTA.
gal80.DELTA. SPAL10::URA3 GAL1::HIS3::lys2 (see Kumar et al., J.
Biol. Chem. 272:13548-13554 (1997); Vidal et al., Proc. Natl. Acad.
Sci. USA, 93:10315-10320 (1996)). Such strains are generally
available in the research community, and can also be obtained by
simple yeast genetic manipulation. See, e.g., The Yeast Two-Hybrid
System, Bartel and Fields, eds., pages 173-182, Oxford University
Press, New York, N.Y., 1997.
[0161] In addition, the following yeast strains are commercially
available:
[0162] Y190 strain which is available from Clontech, Palo Alto,
Calif. and has the genotype MAT.alpha. gal4 gal80 his3.DELTA.200
trp1-901 ade2-101 ura3-52 leu2-3, 112
URA3::GAL1-lacZLYS2::GAL1-HIS3 cyh.sup.r; and
[0163] YRG-2 Strain which is available from Stratagene, La Jolla,
Calif. and has the genotype MAT.alpha. ura3-52 his3-200 ade2-101
lys2-801 trp1-901 leu2-3, 112 gal4-542 gal80-538 LYS2::GAL1-HIS3
URA3:: GAL1/CYC1-lacZ.
[0164] In fact, different versions of vectors and host strains
specially designed for yeast two-hybrid system analysis are
available in kits from commercial vendors such as Clontech, Palo
Alto, Calif. and Stratagene, La Jolla, Calif., all of which can be
modified for use in the present invention.
5.3.1.2. Reporters
[0165] Generally, in a transcription-based two-hybrid assay, the
interaction between a bait fusion protein and a prey fusion protein
brings the DNA-binding domain and the transcription-activation
domain into proximity forming a functional transcriptional factor
that acts on a specific promoter to drive the expression of a
reporter protein. The transcription activation domain and the
DNA-binding domain may be selected from various known
transcriptional activators, e.g., GAL4, GCN4, ARD1, the human
estrogen receptor, E. coli LexA protein, herpes simplex virus VP16
(Triezenberg et al., Genes Dev. 2:718-729 (1988)), the E. coli B42
protein (acid blob, see Gyuris et al., Cell, 75:791-803 (1993)),
NF-kB p65, and the like. The reporter gene and the promoter driving
its transcription typically are incorporated into a separate
reporter vector. Alternatively, the host cells are engineered to
contain such a promoter-reporter gene sequence in their
chromosomes. Thus, the interaction or lack of interaction between
two interacting protein members of a protein complex can be
determined by detecting or measuring changes in the reporter in the
assay system. Although the reporters and selection markers can be
of similar types and used in a similar manner in the present
invention, the reporters and selection markers should be carefully
selected in a particular detection assay such that they are
distinguishable from each other and do not interfere with each
other's function.
[0166] Many different types reporters are useful in the screening
assays. For example, a reporter protein may be a fusion protein
having an epitope tag fused to a protein. Commonly used and
commercially available epitope tags include sequences derived from,
e.g., influenza virus hemagglutinin (HA), Simian Virus 5 (V5),
polyhistidine (6xHis), c-myc, lacZ, GST, and the like. Antibodies
specific to these epitope tags are generally commercially
available. Thus, the expressed reporter can be detected using an
epitope-specific antibody in an immunoassay.
[0167] In another embodiment, the reporter is selected such that it
can be detected by a color-based assay. Examples of such reporters
include, e.g., the lacZ protein (.beta.-galactosidase), the green
fluorescent protein (GFP), which can be detected by fluorescence
assay and sorted by flow-activated cell sorting (FACS) (See Cubitt
et al., Trends Biochem. Sci., 20:448-455 (1995)), secreted alkaline
phosphatase, horseradish peroxidase, the blue fluorescent protein
(BFP), and luciferase photoproteins such as aequorin, obelin,
mnemiopsin, and berovin (See U.S. Pat. No. 6,087,476, which is
incorporated herein by reference).
[0168] Alternatively, an auxotrophic factor is used as a reporter
in a host strain deficient in the auxotrophic factor. Thus,
suitable auxotrophic reporter genes include, but are not limited
to, URA3, HIS3, TRP1, LEU2, LYS2, ADE2, and the like. For example,
yeast cells containing a mutant URA3 gene can be used as host cells
(Ura.sup.-phenotype). Such cells lack URA3-encoded functional
orotidine-5'-phosphate decarboxylase, an enzyme required by yeast
cells for the biosynthesis of uracil. As a result, the cells are
unable to grow on a medium lacking uracil. However, wild-type
orotidine-5'-phosphate decarboxylase catalyzes the conversion of a
non-toxic compound 5-fluoroorotic acid (5-FOA) to a toxic product,
5-fluorouracil. Thus, yeast cells containing a wild-type URA3 gene
are sensitive to 5-FOA and cannot grow on a medium containing
5-FOA. Therefore, when the interaction between the interacting
protein members in the fusion proteins results in the expression of
active orotidine-5'-phosphate decarboxylase, the Ura.sup.-
(Foa.sup.R) yeast cells will be able to grow on a uracil deficient
medium (SC-Ura plates). However, such cells will not survive on a
medium containing 5-FOA. Thus, protein-protein interactions can be
detected based on cell growth.
[0169] Additionally, antibiotic resistance reporters can also be
employed in a similar manner. In this respect, host cells sensitive
to a particular antibiotic are used. Antibiotics resistance
reporters include, for example, the chloramphenicol acetyl
transferase (CAT) gene and the kan.sup.R gene, which confer
resistance to G418 in eukaryotes, and kanamycin in prokaryotes,
respectively.
5.3.1.3. Screening Assays for Interaction Antagonists
[0170] The screening assays of the present invention are useful in
identifying compounds capable of interfering with or disrupting or
dissociating protein-protein interactions between APOA1, or a
mutant form thereof, and a protein selected from the group
consisting of PRA1, GOLGIN-84, Syntaxin 2, APOB and FLJ20724, or a
mutant form thereof. For example, APOA1, or a mutant form thereof,
and its interacting partners, or mutant forms thereof, are believed
to play a role in cholesterol transport and lipid metabolism, and
thus are involved in dementia such as Alzheimer's disease and
cardiovascular diseases such as coronary heart disease,
atherosclerosis, hypercholesterolemia, Tangier disease and
amyloidosis. It may be possible to ameliorate or alleviate the
diseases or disorders in a patient by interfering with or
dissociating normal interactions between APOA1 and one of PRA1,
GOLGIN-84, Syntaxin 2, APOB and FLJ20724. Alternatively, if the
disease or disorder is associated with increased expression of
APOA1 and/or one of the APOA1-interacting proteins in accordance
with the present invention, then the disease may be treated or
prevented by weakening or dissociating the interaction between
APOA1 and the APOA1-interacting protein in patients. In addition,
if a disease or disorder is associated with mutant forms of
APOA1and/or one of the APOA1-interacting proteins that lead to
strengthened protein-protein interaction therebetween, then the
disease or disorder may be treated with a compound that weakens or
interferes with the interaction between the mutant form of APOA1
and/or the APOA1-interacting protein(s).
[0171] In a screening assay for an interaction antagonist, APOA1
(or a homologue, fragment or derivative thereof), or a mutant form
of APOA1 (or a homologue, fragment or derivative thereof), and an
APOA1-interacting protein (or a homologue, fragment or derivative
thereof), or a mutant form of an APOA1-interacting protein (or a
homologue, fragment or derivative thereof), are used as test
proteins expressed in the form of fusion proteins as described
above for purposes of a two-hybrid assay. The fusion proteins are
expressed in a host cell and allowed to interact with each other in
the presence of one or more test compounds.
[0172] In a preferred embodiment, a counterselectable marker is
used as a reporter such that a detectable signal (e.g., appearance
of color or fluorescence, or cell survival) is present only when
the test compound is capable of interfering with the interaction
between the two test proteins. In this respect, the reporters used
in various "reverse two-hybrid systems" known in the art may be
employed. Reverse two-hybrid systems are disclosed in, e.g., U.S.
Pat. Nos. 5,525,490; 5,733,726; 5,885,779; Vidal et al., Proc.
Natl. Acad. Sci. USA, 93:10315-10320 (1996); and Vidal et al.,
Proc. Natl. Acad. Sci. USA, 93:10321-10326 (1996), all of which are
incorporated herein by reference.
[0173] Examples of suitable counterselectable reporters useful in a
yeast system include the URA3 gene (encoding
orotidine-5'-decarboxylase, which converts 5-fluroorotic acid
(5-FOA) to the toxic metabolite 5-fluorouracil), the CAN1 gene
(encoding arginine permease, which transports toxic arginine analog
canavanine into yeast cells), the GAL1gene (encoding galactokinase,
which catalyzes the conversion of 2-deoxygalactose to toxic
2-deoxygalactose-1-phosphate), the LYS2 gene (encoding
.alpha.-aminoadipate reductase, which renders yeast cells unable to
grow on a medium containing .alpha.-aminoadipate as the sole
nitrogen source), the MET15 gene (encoding O-acetylhomoserine
sulfhydrylase, which confers on yeast cells sensitivity to methyl
mercury), and the CYH2 gene (encoding L29 ribosomal protein, which
confers sensitivity to cycloheximide). In addition, any known
cytotoxic agents including cytotoxic proteins such as the
diphtheria toxin (DTA) catalytic domain can also be used as
counterselectable reporters. See U.S. Pat. No. 5,733,726. DTA
causes the ADP-ribosylation of elongation factor-2 and thus
inhibits protein synthesis and causes cell death. Other examples of
cytotoxic agents include ricin, Shiga toxin, and exotoxin A of
Pseudomonas aeruginosa.
[0174] For example, when the URA3 gene is used as a
counterselectable reporter gene, yeast cells containing a mutant
URA3 gene can be used as host cells (Ura.sup.-Foa.sup.R phenotype)
for the in vivo assay. Such cells lack URA3-encoded functional
orotidine-5'-phosphate decarboxylase, an enzyme required for the
biosynthesis of uracil. As a result, the cells are unable to grow
on media lacking uracil. However, because of the absence of a
wild-type orotidine-5'-phosphate decarboxylase, the yeast cells
cannot convert non-toxic 5-fluoroorotic acid (5-FOA) to a toxic
product, 5-fluorouracil. Thus, such yeast cells are resistant to
5-FOA and can grow on a medium containing 5-FOA. Therefore, for
example, to screen for a compound capable of disrupting
interactions between APOA1 (or a homologue, fragment or derivative
thereof), or a mutant form of APOA1(or a homologue, fragment or
derivative thereof), and PRA1 (or a homologue, fragment or
derivative thereof), or a mutant form of PRA1 (or a homologue,
fragment or derivative thereof), APOA1 (or a homologue, fragment or
derivative thereof) can be expressed as a fusion protein with a
DNA-binding domain of a suitable transcription activator while PRA1
(or a homologue, fragment or derivative thereof) is expressed as a
fusion protein with a transcription activation domain of a suitable
transcription activator. In the host strain, the reporter URA3 gene
may be operably linked to a promoter specifically responsive to the
association of the transcription activation domain and the
DNA-binding domain. After the fusion proteins are expressed in the
Ura.sup.-Foa.sup.R yeast cells, an in vivo screening assay can be
conducted in the presence of a test compound with the yeast cells
being cultured on a medium containing uracil and 5-FOA. If the test
compound does not disrupt the interaction between APOA1 and PRA1,
active URA3 gene product, i.e., orotidine-5'-decarboxylase, which
converts 5-FOA to toxic 5-fluorouracil, is expressed. As a result,
the yeast cells cannot grow. On the other hand, when the test
compound disrupts the interaction between APOA1 and PRA1, no active
orotidine-5'-decarboxylase is produced in the host yeast cells.
Consequently, the yeast cells will survive and grow on the
5-FOA-containing medium. Therefore, compounds capable of
interfering with or dissociating the interaction between APOA1 and
PRA1 can thus be identified based on colony formation.
[0175] As will be apparent, the screening assay of the present
invention can be applied in a format appropriate for large-scale
screening. For example, combinatorial technologies can be employed
to construct combinatorial libraries of small organic molecules or
small peptides. See generally, e.g., Kenan et al., Trends Biochem.
Sc., 19:57-64 (1994); Gallop et al., J. Med. Chem., 37:1233-1251
(1994); Gordon et al., J. Med. Chem., 37:1385-1401 (1994); Ecker et
al., Biotechnology, 13:351-360 (1995). Such combinatorial libraries
of compounds can be applied to the screening assay of the present
invention to isolate specific modulators of particular
protein-protein interactions. In the case of random peptide
libraries, the random peptides can be co-expressed with the fusion
proteins of the present invention in host cells and assayed in
vivo. See e.g., Yang et al., Nucl. Acids Res., 23:1152-1156 (1995).
Alternatively, they can be added to the culture medium for uptake
by the host cells.
[0176] Conveniently, yeast mating is used in an in vivo screening
assay. For example, haploid cells of .alpha.-mating type expressing
one fusion protein as described above are mated with haploid cells
of .alpha.-mating type expressing the other fusion protein. Upon
mating, the diploid cells are spread on a suitable medium to form a
lawn. Drops of test compounds can be deposited onto different areas
of the lawn. After culturing the lawn for an appropriate period of
time, drops containing a compound capable of modulating the
interaction between the particular test proteins in the fusion
proteins can be identified by stimulation or inhibition of growth
in the vicinity of the drops.
[0177] The screening assays of the present invention for
identifying compounds capable of modulating protein-protein
interactions can also be fine-tuned by various techniques to adjust
the thresholds or sensitivity of the positive and negative
selections. Mutations can be introduced into the reporter proteins
to adjust their activities. The uptake of test compounds by the
host cells can also be adjusted. For example, yeast high uptake
mutants such as the erg6 mutant strains can facilitate yeast uptake
of the test compounds. See Gaber et al., Mol. Cell. Biol.,
9:3447-3456 (1989). Likewise, the uptake of the selection compounds
such as 5-FOA, 2-deoxygalactose, cycloheximide,
.alpha.-aminoadipate, and the like can also be fine-tuned.
5.3.1.4. Screening Assays for Interaction Agonists
[0178] The screening assays of the present invention can also be
used in identifying compounds that trigger or initiate, enhance or
stabilize protein-protein interactions between APOA1, or a mutant
form thereof, and a protein selected from the group consisting of
PRA1, GOLGIN-84, Syntaxin 2, APOB and FLJ20724, or a mutant
thereof. For example, if a disease or disorder is associated with
decreased expression of APOA1and/or a member of selected from the
group of PRA1, GOLGIN-84, Syntaxin 2, APOB and FLJ20724, then the
disease or disorder may be treated or prevented by strengthening or
stabilizing the interaction between APOA1 and the APOA1-interacting
member in patients. Alternatively, if a disease or disorder is
associated with mutant forms of APOA1 and/or mutant forms of an
APOA1-interacting protein that lead to weakened or abolished
protein-protein interaction therebetween, then the disease or
disorder may be treated with a compound that initiates or
stabilizes the interaction between the mutant forms of APOA1 and/or
the mutant forms of APOA1-interacting protein(s).
[0179] Thus, a screening assay can be performed in the same manner
as described above, except that a positively selectable marker is
used. For example, APOA1 (or a homologue, fragment, or derivative
thereof), or a mutant form of APOA1 (or a homologue, fragment, or
derivative thereof), and a protein selected from the group
consisting of PRA1, GOLGIN-84, Syntaxin 2, APOB and FLJ20724 (or a
homologue, fragment, or derivative thereof), or a mutant form of a
protein selected from the group consisting of PRA1, GOLGIN-84,
Syntaxin 2, APOB and FLJ20724 (or a homologue, fragment, or
derivative thereof), are used as test proteins expressed in the
form of fusion proteins as described above for purposes of a
two-hybrid assay. The fusion proteins are expressed in host cells
and are allowed to interact with each other in the presence of one
or more test compounds.
[0180] A gene encoding a positively selectable marker such as the
lacZ protein may be used as a reporter gene such that when a test
compound enables or enhances the interaction between APOA1 (or a
homologue, fragment, or derivative thereof), or a mutant form of
APOA1 (or a homologue, fragment, or derivative thereof), and a
protein selected from the group consisting of PRA1, GOLGIN-84,
Syntaxin 2, APOB and FLJ20724 (or a homologue, fragment, or
derivative thereof), or a mutant form of a protein selected from
the group consisting of PRA1, GOLGIN-84, Syntaxin 2, APOB and
FLJ20724 (or a homologue, fragment, or derivative thereof), the
lacZ protein, i.e., .beta.-galatosidase, is expressed. As a result,
the compound may be identified based on the appearance of a blue
color when the host cells are cultured in a medium containing
X-Gal.
[0181] Generally, a control assay is performed in which the above
screening assay is conducted in the absence of the test compound.
The result is then compared with that obtained in the presence of
the test compound.
5.4. Optimization of the Identified Compounds
[0182] Once the test compounds are selected capable of modulating
the interaction between PRA1 and a protein selected from PRA1,
GOLGIN-84, Syntaxin 2, APOB and FLJ20724, or modulating PRA1, or
PRA1, GOLGIN-84, Syntaxin 2, APOB and FLJ20724, a data set
including data defining the identity or characteristics of the test
compounds can be generated. The data set may include information
relating to the properties of a selected test compound, e.g.,
chemical structure, chirality, molecular weight, melting point,
etc. Alternatively, the data set may simply include assigned
identification numbers understood by the researchers conducting the
screening assay and/or researchers receiving the data set as
representing specific test compounds. The data or information can
be cast in a transmittable form that can be communicated or
transmitted to other researchers, particularly researchers in a
different country. Such a transmittable form can vary and can be
tangible or intangible. For example, the data set defining one or
more selected test compounds can be embodied in texts, tables,
diagrams, molecular structures, photographs, charts, images or any
other visual forms. The data or information can be recorded on a
tangible media such as paper or embodied in computer-readable forms
(e.g., electronic, electromagnetic, optical or other signals). The
data in a computer-readable form can be stored in a computer usable
storage medium (e.g., floppy disks, magnetic tapes, optical disks,
and the like) or transmitted directly through a communication
infrastructure. In particular, the data embodied in electronic
signals can be transmitted in the form of email or posted on a
website on the Internet or Intranet. In addition, the information
or data on a selected test compound can also be recorded in an
audio form and transmitted through any suitable media, e.g., analog
or digital cable lines, fiber optic cables, etc., via telephone,
facsimile, wireless mobile phone, Internet phone and the like.
[0183] Thus, the information and data on a test compound selected
in a screening assay described above or by virtual screening as
discussed below can be produced anywhere in the world and
transmitted to a different location. For example, when a screening
assay is conducted offshore, the information and data on a selected
test compound can be generated and cast in a transmittable form as
described above. The data and information in a transmittable form
thus can be imported into the U.S. or transmitted to any other
countries, where the data and information may be used in further
testing the selected test compound and/or in modifying and
optimizing the selected test compound to develop lead compounds for
testing in clinical trials.
[0184] Compounds can also be selected based on structural models of
the target protein or protein complex and/or test compounds. In
addition, once an effective compound is identified, structural
analogs or mimetics thereof can be produced based on rational drug
design with the aim of improving drug efficacy and stability, and
reducing side effects. Methods known in the art for rational drug
design can be used in the present invention. See, e.g., Hodgson et
al., Bio/Technology, 9:19-21 (1991); U.S. Pat. Nos. 5,800,998 and
5,891,628, all of which are incorporated herein by reference. An
example of rational drug design is the development of HIV protease
inhibitors. See Erickson et al., Science, 249:527-533 (1990).
[0185] In this respect, structural information on the target
protein or protein complex is obtained. Preferably, atomic
coordinates defining a three-dimensional structure of the target
protein or protein complex can be obtained. For example, each of
the interacting pair can be expressed and purified. The purified
interacting protein pairs are then allowed to interact with each
other in vitro under appropriate conditions. Optionally, the
interacting protein complex can be stabilized by crosslinking or
other techniques. The interacting complex can be studied using
various biophysical techniques including, e.g., X-ray
crystallography, NMR, computer modeling, mass spectrometry, and the
like. Likewise, structural information can also be obtained from
protein complexes formed by interacting proteins and a compound
that initiates or stabilizes the interaction of the proteins.
Methods for obtaining such atomic coordinates by X-ray
crystallography, NMR, and the like are known in the art and the
application thereof to the target protein or protein complex of the
present invention should be apparent to skilled persons in the art
of structural biology. See Smyth and Martin, Mol. Pathol., 53:8-14
(2000); Oakley and Wilce, Clin. Exp. Pharmacol. Physiol.,
27(3):145-151 (2000); Ferentz and Wagner, Q. Rev. Biophys.,
33:29-65 (2000); Hicks, Curr. Med. Chem., 8(6):627-650 (2001); and
Roberts, Curr. Opin. Biotechnol., 10:42-47 (1999).
[0186] In addition, understanding of the interaction between the
proteins of interest in the presence or absence of a modulator can
also be derived from mutagenesis analysis using yeast two-hybrid
system or other methods for detection protein-protein interaction.
In this respect, various mutations can be introduced into the
interacting proteins and the effect of the mutations on
protein-protein interaction examined by a suitable method such as
the yeast two-hybrid system.
[0187] Various mutations including amino acid substitutions,
deletions and insertions can be introduced into a protein sequence
using conventional recombinant DNA technologies. Generally, it is
particularly desirable to decipher the protein binding sites. Thus,
it is important that the mutations introduced only affect
protein-protein interaction and cause minimal structural
disturbances. Mutations are preferably designed based on knowledge
of the three-dimensional structure of the interacting proteins.
Preferably, mutations are introduced to alter charged amino acids
or hydrophobic amino acids exposed on the surface of the proteins,
since ionic interactions and hydrophobic interactions are often
involved in protein-protein interactions. Alternatively, the
"alanine scanning mutagenesis" technique is used. See Wells, et
al., Methods Enzymol., 202:301-306 (1991); Bass et al., Proc. Natl.
Acad. Sci. USA, 88:4498-4502 (1991); Bennet et al., J. Biol. Chem.,
266:5191-5201 (1991); Diamond et al., J. Virol., 68:863-876 (1994).
Using this technique, charged or hydrophobic amino acid residues of
the interacting proteins are replaced by alanine, and the effect on
the interaction between the proteins is analyzed using e.g., the
yeast two-hybrid system. For example, the entire protein sequence
can be scanned in a window of five amino acids. When two or more
charged or hydrophobic amino acids appear in a window, the charged
or hydrophobic amino acids are changed to alanine using standard
recombinant DNA techniques. The thus mutated proteins are used as
"test proteins" in the above-described two-hybrid assays to examine
the effect of the mutations on protein-protein interaction.
Preferably, the mutagenesis analysis is conducted both in the
presence and in the absence of an identified modulator compound. In
this manner, the domains or residues of the proteins important to
protein-protein interaction and/or the interaction between the
modulator compound and the interacting proteins can be
identified.
[0188] Based on the information obtained, structural relationships
between the interacting proteins, as well as between the identified
modulators and the interacting proteins are elucidated. For
example, for the identified modulators (i.e., lead compounds), the
three-dimensional structure and chemical moieties critical to their
modulating effect on the interacting proteins are revealed. Using
this information and various techniques know in the art of
molecular modeling (i.e., simulated annealing), medicinal chemists
can then design analog compounds that might be more effective
modulators of the protein-protein interactions of the present
invention. For example, the analog compounds might show more
specific or tighter binding to their targets, and thereby might
exhibit fewer side effects, or might have more desirable
pharmacological characteristics (e.g., greater solubility).
[0189] In addition, if the lead compound is a peptide, it can also
be analyzed by the alanine scanning technique and/or the two-hybrid
assay to determine the domains or residues of the peptide important
to its modulating effect on particular protein-protein
interactions. The peptide compound can be used as a lead molecule
for rational design of small organic molecules or peptide mimetics.
See Huber et al., Curr. Med. Chem., 1:13-34 (1994).
[0190] The domains, residues or moieties critical to the modulating
effect of the identified compound constitute the active region of
the compound known as its "pharmacophore." Once the pharmacophore
has been elucidated, a structural model can be established by a
modeling process that may incorporate data from NMR analysis, X-ray
diffraction data, alanine scanning, spectroscopic techniques and
the like. Various techniques including computational analysis
(e.g., molecular modeling and simulated annealing), similarity
mapping and the like can all be used in this modeling process. See
e.g., Perry et al., in OSAR: Quantitative Structure-Activity
Relationships in Drug Design, pp.189-193, Alan R. Liss, Inc., 1989;
Rotivinen et al., Acta Pharmaceutical Fennica, 97:159-166 (1988);
Lewis et al., Proc. R. Soc. Lond., 236:125-140 (1989); McKinaly et
al., Annu. Rev. Pharmacol. Toxiciol., 29:111-122 (1989). Commercial
molecular modeling systems available from Polygen Corporation,
Waltham, Mass., include the CHARMm program, which performs energy
minimization and molecular dynamics functions, and QUANTA program
which performs construction, graphic modeling and analysis of
molecular structure. Such programs allow interactive construction,
modification and visualization of molecules. Other computer
modeling programs are also available from BioDesign, Inc.
(Pasadena, Calif.), Hypercube, Inc. (Cambridge, Ontario), and
Allelix, Inc. (Mississauga, Ontario, Canada).
[0191] A template can be formed based on the established model.
Various compounds can then be designed by linking various chemical
groups or moieties to the template. Various moieties of the
template can also be replaced. In addition, in the case of a
peptide lead compound, the peptide or mimetics thereof can be
cyclized, e.g., by linking the N-terminus and C-terminus together,
to increase its stability. These rationally designed compounds are
further tested. In this manner, pharmacologically acceptable and
stable compounds with improved efficacy and reduced side effect can
be developed. The compounds identified in accordance with the
present invention can be incorporated into a pharmaceutical
formulation suitable for administration to an individual.
[0192] In addition, the structural models or atomic coordinates
defining a three-dimensional structure of the target protein or
protein complex can also be used in virtual screen to select
compounds capable of modulating the target protein or protein
complex. Various methods of computer-based virtual screen using
atomic coordinates are generally known in the art. For example,
U.S. Pat. No. 5,798,247 (which is incorporated herein by reference)
discloses a method of identifying a compound (specifically, an
interleukin converting enzyme inhibitor) by determining binding
interactions between an organic compound and binding sites of a
binding cavity within the target protein. The binding sites are
defined by atomic coordinates.
[0193] The compounds designed or selected based on rational drug
design or virtual screen can be tested for their ability to
modulate (interfere with or strengthen) the interaction between the
interacting partners within the protein complexes of the present
invention. In addition, the compounds can also be further tested
for their ability to modulate (inhibit or enhance) cellular
functions such as cholesterol transport and lipid metabolism in
cells as well as their effectiveness in treating diseases such as
Alzheimer's disease and cardiovascular disease.
6. Therapeutic Applications
[0194] As described above, the interactions between APOA1 and the
APOA1-interacting proteins suggest that these proteins and/or the
protein complexes formed by them may be involved in common
biological processes and disease pathways. The protein complexes
may mediate the functions of APOA1 and the APOA1-interacting
proteins in the biological processes or disease pathways. Thus, one
may modulate such biological processes or treat diseases by
modulating the functions and activities of APOA1, an
APOA1-interacting protein, and/or a protein complex comprising some
combination of these proteins. As used herein, modulating APOA1, an
APOA1-interacting protein, or a protein complex comprising some
combination of these proteins means altering (enhancing or
reducing) the concentrations or activities of the proteins or
protein complexes, e.g., increasing the concentrations of APOA1, an
APOA1-interacting protein or a protein complex comprising some
combination of these proteins, enhancing or reducing their
biological activities, increasing or decreasing their stability,
altering their affinity or specificity to certain other biological
molecules, etc. For example, an APOA1-containing protein complex of
the present invention or its members thereof may be involved in
cholesterol transport and lipid metabolism. Thus, assays such as
those described in Section 4 may be used in determining the effect
of an aberration in a particular APOA1-containing complex or an
interacting member thereof on cholesterol transport and lipid
metabolism. In addition, it is also possible to determine, using
the same assay methods, the presence or absence of an association
between an APOA1-containing complex or an interacting member
thereof and a physiological disorder or disease such as dementia
such as Alzheimer's disease and cardiovascular diseases such as
coronary heart disease, atherosclerosis, hypercholesterolemia,
Tangier disease and amyloidosis or predisposition to a
physiological disorder or disease.
[0195] Once such associations are established, the diagnostic
methods as described in Section 4 can be used in diagnosing the
disease or disorder, or a patient's predisposition to it. In
addition, various in vitro and in vivo assays may be employed to
test the therapeutic or prophylactic efficacies of the various
therapeutic approaches described in Sections 6.2 and 6.3 that are
aimed at modulating the functions and activities of a particular
APOA1-containing complex of the present invention, or an
interacting member thereof. Similar assays can also be used to test
whether the therapeutic approaches described in Sections 6.2 and
6.3 result in the modulation of cholesterol transport and lipid
metabolism. The cell model or transgenic animal model described in
Section 7 may be employed in the in vitro and in vivo assays.
[0196] In accordance with this aspect of the present invention,
methods are provided for modulating (promoting or inhibiting) an
APOA1-containing protein complex or interacting member thereof. The
human cells can be in in vitro cell or tissue cultures. The methods
are also applicable to human cells in a patient.
[0197] In one embodiment, the concentration of an APOA1-containing
protein complex of the present invention is reduced in the cells.
Various methods can be employed to reduce the concentration of the
protein complex. The protein complex concentration can be reduced
by interfering with the interactions between the interacting
members. For example, compounds capable of interfering with
interactions between APOA1 and a protein selected from the group of
PRA1, GOLGIN-84, Syntaxin 2, APOB and FLJ20724 can be administered
to the cells in vitro or in vivo in a patient. Such compounds can
be compounds capable of binding APOA1 or the protein selected from
PRA1, GOLGIN-84, Syntaxin 2, APOB and FLJ20724. They can also be
antibodies immunoreactive with the APOA1 or the protein selected
from PRA1, GOLGIN-84, Syntaxin 2, APOB and FLJ20724. Also, the
compounds can be small peptides derived from the an
APOA1-interacting protein or mimetics thereof capable of binding
APOA1, or small peptides derived from APOA1 protein or mimetics
thereof capable of binding a protein selected from PRA1, GOLGIN-84,
Syntaxin 2, APOB and FLJ20724.
[0198] In another embodiment, the method of modulating the protein
complex includes inhibiting the expression of APOA1 protein and/or
an APOA1-interacting protein. The inhibition can be at the
transcriptional, translational, or post-translational level. For
example, antisense compounds and ribozyme compounds can be
administered to human cells in cultures or in human bodies. In
addition, RNA interference technologies may also be employed to
administer to cells double-stranded RNA or RNA hairpins capable of
"knocking down" the expression of APOA1 protein and/or an
APOA1-interacting protein.
[0199] In the various embodiments described above, preferably the
concentrations or activities of both APOA1 protein and an
APOA1-interacting protein are reduced or inhibited.
[0200] In yet another embodiment, an antibody selectively
immunoreactive with a protein complex having APOA1 interacting with
a protein selected from PRA1, GOLGIN-84, Syntaxin 2, APOB and
FLJ20724 is administered to cells in vitro or in human bodies to
inhibit the protein complex activities and/or reduce the
concentration of the protein complex in the cells or patient.
6.1. Applicable Diseases
[0201] As discussed above, the interactions between APOA1 and its
interacting partners may be involved in cholesterol transport and
lipid metabolism, and thus in diseases such as Alzheimer's disease
and hypercholesterolemia. Thus, the methods for modulating the
functions and activities of an APOA1-containing protein complex of
the present invention, or an interacting member thereof, may be
employed to modulate cholesterol transport and lipid metabolism. In
addition, the methods may also be used in the treatment or
prevention of diseases and disorders such as dementia such as
Alzheimer's disease and cardiovascular diseases such as coronary
heart disease, atherosclerosis, hypercholesterolemia, Tangier
disease and amyloidosis.
6.2. Inhibiting Protein Complex or Interacting Protein Members
Thereof
[0202] In one aspect of the present invention, methods are provided
for reducing in cells or tissue the concentration and/or activity
of a protein complex identified in accordance with the present
invention that comprises APOA1 and one or more members of the group
PRA1, GOLGIN-84, Syntaxin 2, APOB and FLJ20724. In addition,
methods are also provided for reducing in cells or tissue the
concentration and/or activity of an APOA1-interacting protein
selected from the group PRA1, GOLGIN-84, Syntaxin 2, APOB and
FLJ20724. By reducing the concentration of protein complex and/or
the APOA1-interacting protein concentration(s) and/or inhibiting
the functional activities of the protein complex and/or the APOA1
-interacting protein(s), the diseases involving such protein
complex or APOA1-interacting protein(s) may be treated or
prevented.
6.2.1. Antibody Therapy
[0203] In one embodiment, an antibody may be administered to cells
or tissue in vitro or to patients. The antibody administered may be
immunoreactive with APOA1 or a member of the group PRA1, GOLGIN-84,
Syntaxin 2, APOB and FLJ20724, or protein complexes comprising
APOA1 and a member, or members, of the group PRA1, GOLGIN-84,
Syntaxin 2, APOB and FLJ20724. Suitable antibodies may be
monoclonal or polyclonal that fall within any antibody class, e.g.,
IgG, IgM, IgA, etc. The antibody suitable for this invention may
also take a form of various antibody fragments including, but not
limited to, Fab and F(ab')2, single-chain fragments (scFv), and the
like. In another embodiment, an antibody selectively immunoreactive
with the protein complex formed from APOA1 and one or more
APOA1-interacting protein, or proteins, in accordance with the
present invention is administered to cells or tissue in vitro or in
a patient. In yet another embodiment, an antibody specific to an
APOA1-interacting protein selected from the group PRA1, GOLGIN-84,
Syntaxin 2, APOB and FLJ20724 is administered to cells or tissue in
vitro or in a patient. Methods for making the antibodies of the
present invention should be apparent to a person of skill in the
art, especially in view of the discussions in Section 3 above. The
antibodies can be administered in any suitable form and route as
described in Section 8 below. Preferably, the antibodies are
administered in a pharmaceutical composition together with a
pharmaceutically acceptable carrier.
[0204] Alternatively, the antibodies may be delivered by a
gene-therapy approach. That is, nucleic acids encoding the
antibodies, particularly single-chain fragments (scFv), may be
introduced into cells or tissue in vitro or in a patient such that
desirable antibodies may be produced recombinantly in vivo from the
nucleic acids. For this purpose, the nucleic acids with appropriate
transcriptional and translation regulatory sequences can be
directly administered into the patient. Alternatively, the nucleic
acids can be incorporated into a suitable vector as described in
Sections 2.2 and 5.3.1.1 and delivered into cells or tissue in
vitro or in a patient along with the vector. The expression vector
containing the nucleic acids can be administered directly to cells
or tissue in vitro or in a patient. It can also be introduced into
cells, preferably cells derived from a patient to be treated, and
subsequently delivered into the patient by cell transplantation.
See Section 6.3.2 below.
6.2.2. Antisense Therapy
[0205] In another embodiment, antisense compounds specific to
nucleic acids encoding one or more interacting protein members of a
protein complex identified in the present invention are
administered to cells or tissue in vitro or in a patient to be
therapeutically or prophylactically treated. The antisense
compounds should specifically inhibit the expression of the one or
more interacting protein members. As is known in the art, antisense
drugs generally act by hybridizing to a particular target nucleic
acid thus blocking gene expression. Methods for designing antisense
compounds and using such compounds in treating diseases are well
known and well developed in the art. For example, the antisense
drug Vitravene.RTM. (fomivirsen), a 21-base long oligonucleotide,
has been successfully developed and marketed by Isis
Pharmaceuticals, Inc. for treating cytomegalovirus (CMV)-induced
retinitis.
[0206] Any methods for designing and making antisense compounds may
be used for purpose of the present invention. See generally,
Sanghvi et al., eds., Antisense Research and Applications, CRC
Press, Boca Raton, 1993. Typically, antisense compounds are
oligonucleotides designed based on the nucleotide sequence of the
mRNA or gene of one or more target proteins, e.g., the interacting
protein members of a particular protein complex of the present
invention. In particular, antisense compounds can be designed to
specifically hybridize to a particular region of the gene sequence
or mRNA of one or more of the interacting protein members to
modulate (increase or decrease), replication, transcription, or
translation. As used herein, the term "specifically hybridize" or
paraphrases thereof means a sufficient degree of complementarity or
pairing between an antisense oligo and a target DNA or mRNA such
that stable and specific binding occurs therebetween. In
particular, 100% complementary or pairing is not required. Specific
hybridization takes place when sufficient hybridization occurs
between the antisense compound and its intended target nucleic
acids in the substantial absence of non-specific binding of the
antisense compound to non-target sequences under predetermined
conditions, e.g., for purposes of in vivo treatment, preferably
under physiological conditions. Preferably, specific hybridization
results in the interference with normal expression of the target
DNA or mRNA.
[0207] For example, antisense oligonucleotides can be designed to
specifically hybridize to target genes, in regions critical for
regulation of transcription; to pre-mRNAs, in regions critical for
correct splicing of nascent transcripts; and to mature mRNAs, in
regions critical for translation initiation or mRNA stability and
localization.
[0208] As is generally known in the art, commonly used
oligonucleotides are oligomers or polymers of ribonucleotides or
deoxyribonucleotides, that are composed of a naturally-occurring
nitrogenous base, a sugar (ribose or deoxyribose) and a phosphate
group. In nature, the nucleotides are linked together by
phosphodiester bonds between the 3' and 5' positions of neighboring
sugar moieties. However, it is noted that the term
"oligonucleotides" also encompasses various non-naturally occurring
mimetics and derivatives, i.e., modified forms, of naturally
occurring oligonucleotides as described below. Typically an
antisense compound of the present invention is an oligonucleotide
having from about 6 to about 200, and preferably from about 8 to
about 30 nucleoside bases.
[0209] The antisense compounds preferably contain modified
backbones or non-natural intemucleoside linkages, including but not
limited to, modified phosphorous-containing backbones and
non-phosphorous backbones such as morpholino backbones; siloxane,
sulfide, sulfoxide, sulfone, sulfonate, sulfonamide, and sulfamate
backbones; formacetyl and thioformacetyl backbones;
alkene-containing backbones; methyleneimino and methylenehydrazino
backbones; amide backbones, and the like.
[0210] Examples of modified phosphorous-containing backbones
include, but are not limited to phosphorothioates,
phosphorodithioates, chiral phosphorothioates, phosphotriesters,
aminoalkylphosphotriesters, alkyl phosphonates,
thionoalkylphosphonates, phosphinates, phosphoramidates,
thionophosphoramidates, thionoalkylphosphotriesters, and
boranophosphates and various salt forms thereof. See e.g., U.S.
Pat. Nos. 3,687,808; 4,469,863; 4,476,301; 5,023,243; 5,177,196;
5,188,897; 5,264,423; 5,276,019; 5,278,302; 5,286,717; 5,321,131;
5,399,676; 5,405,939; 5,453,496; 5,455,233; 5,466,677; 5,476,925;
5,519,126; 5,536,821; 5,541,306; 5,550,111; 5,563,253; 5,571,799;
5,587,361; and 5,625,050, each of which is herein incorporated by
reference.
[0211] Examples of the non-phosphorous containing backbones
described above are disclosed in, e.g., U.S. Pat. Nos. 5,034,506;
5,185,444; 5,214,134; 5,216,141; 5,235,033; 5,264,562; 5,264,564;
5,405,938; 5,434,257; 5,470,967; 5,489,677; 5,541,307; 5,561,225;
5,596,086; 5,610,289; 5,602,240; 5,608,046; 5,610,289; 5,618,704;
5,623,070; 5,663,312; 5,677,437; and 5,677,439, each of which is
herein incorporated by reference.
[0212] Another useful modified oligonucleotide is peptide nucleic
acid (PNA), in which the sugar-backbone of an oligonucleotide is
replaced with an amide containing backbone, e.g., an
aminoethylglycine backbone. See U.S. Pat. Nos. 5,539,082 and
5,714,331; and Nielsen et al., Science, 254, 1497-1500 (1991), all
of which are incorporated herein by reference. PNA antisense
compounds are resistant to RNase H digestion and thus exhibit
longer half-life. In addition, various modifications may be made in
PNA backbones to impart desirable drug profiles such as better
stability, increased drug uptake, higher affinity to target nucleic
acid, etc.
[0213] Alternatively, the antisense compounds are oligonucleotides
containing modified nucleosides, i.e., modified purine or
pyrimidine bases, e.g., 5-substituted pyrimidines,
6-azapyrimidines, and N-2, N-6 and O-substituted purines, and the
like. See e.g., U.S. Pat. Nos. 3,687,808; 4,845,205; 5,130,302;
5,175,273; 5,367,066; 5,432,272; 5,459,255; 5,484,908; 5,502,177;
5,525,711; 5,587,469; 5,594,121; 5,596,091; 5,681,941; and
5,750,692, each of which is incorporated herein by reference in its
entirety.
[0214] In addition, oligonucleotides with substituted or modified
sugar moieties may also be used. For example, an antisense compound
may have one or more 2'-O-methoxyethyl sugar moieties. See e.g.,
U.S. Pat. Nos. 4,981,957; 5,118,800; 5,319,080; 5,393,878;
5,446,137; 5,466,786; 5,514,785; 5,567,811; 5,576,427; 5,591,722;
5,610,300; 5,627,053, 5,639,873; 5,646,265; 5,658,873; 5,670,633;
and 5,700,920, each of which is herein incorporated by
reference.
[0215] Other types of oligonucleotide modifications are also useful
including linking an oligonucleotide to a lipid, phospholipid or
cholesterol moiety, cholic acid, thioether, aliphatic chain,
polyamine, polyethylene glycol (PEG), or a protein or peptide. The
modified oligonucleotides may exhibit increased uptake into cells,
and improved stability, i.e., resistance to nuclease digestion and
other biodegradations. See e.g., U.S. Pat. No. 4,522,811; Burnham,
Am. J. Hosp. Pharm., 15:210-218 (1994).
[0216] Antisense compounds can be synthesized using any suitable
methods known in the art. In fact, antisense compounds may be
custom made by commercial suppliers. Alternatively, antisense
compounds may be prepared using DNA synthesizers available
commercially from various vendors, e.g., Applied Biosystems Group
of Norwalk, Conn.
[0217] The antisense compounds can be formulated into a
pharmaceutical composition with suitable carriers and administered
into cells or tissue in vitro or in a patient using any suitable
route of administration. Alternatively, the antisense compounds may
also be used in a "gene-therapy" approach. That is, the
oligonucleotide is subcloned into a suitable vector and transformed
into human cells. The antisense oligonucleotide is then produced in
vivo through transcription. Methods for gene therapy are disclosed
in Section 6.3.2 below.
6.2.3. Ribozyme Therapy
[0218] In another embodiment, an enzymatic RNA or ribozyme is
designed to target the nucleic acids encoding one or more of the
interacting protein members of the protein complex of the present
invention. Ribozymes are RNA molecules possessing enzymatic
activity. One class of ribozymes is capable of repeatedly cleaving
other separate RNA molecules into two or more pieces in a
nucleotide base sequence specific manner. See Kim et al., Proc.
Natl. Acad. of Sci. USA, 84:8788 (1987); Haseloff and Gerlach,
Nature, 334:585 (1988); and Jefferies et al., Nucleic Acid Res.,
17:1371 (1989). Such ribozymes typically have two functional
domains: a catalytic domain and a binding sequence that guides the
binding of ribozymes to a target RNA through complementary
base-pairing. Once a specifically-designed ribozyme is bound to a
target mRNA, it enzymatically cleaves the target mRNA, typically
reducing its stability and destroying its ability to direct
translation of an encoded protein. After a ribozyme has cleaved its
RNA target, it is released from that target RNA and thereafter can
bind and cleave another target. That is, a single ribozyme molecule
can repeatedly bind and cleave new targets. Therefore, one
advantage of ribozyme treatment is that a lower amount of exogenous
RNA is required as compared to conventional antisense therapies. In
addition, ribozymes exhibit less affinity to mRNA targets than
DNA-based antisense oligonucleotides, and therefore are less prone
to bind to wrong targets.
[0219] In accordance with the present invention, a ribozyme may
target any portion of the mRNA of one or more interacting protein
members including APOA1, and PRA1, GOLGIN-84, Syntaxin 2, APOB and
FLJ20724. Methods for selecting a ribozyme target sequence and
designing and making ribozymes are generally known in the art. See
e.g., U.S. Pat. Nos. 4,987,071; 5,496,698; 5,525,468; 5,631,359;
5,646,020; 5,672,511; and 6,140,491, each of which is incorporated
herein by reference in its entirety. For example, suitable
ribozymes may be designed in various configurations such as
hammerhead motifs, hairpin motifs, hepatitis delta virus motifs,
group I intron motifs, or RNase P RNA motifs. See e.g., U.S. Pat.
Nos. 4,987,071; 5,496,698; 5,525,468; 5,631,359; 5,646,020;
5,672,511; and 6,140,491; Rossi et al., AIDS Res. Human
Retroviruses 8:183 (1992); Hampel and Tritz, Biochemistry 28:4929
(1989); Hampel et al., Nucleic Acids Res., 18:299 (1990); Perrotta
and Been, Biochemistry 31:16 (1992); and Guerrier-Takada et al.,
Cell, 35:849 (1983).
[0220] Ribozymes can be synthesized by the same methods used for
normal RNA synthesis. For example, such methods are disclosed in
Usman et al., J. Am. Chem. Soc., 109:7845-7854 (1987) and Scaringe
et al., Nucleic Acids Res., 18:5433-5441 (1990). Modified ribozymes
may be synthesized by the methods disclosed in, e.g., U.S. Pat. No.
5,652,094; International Publication Nos. WO 91/03162; WO 92/07065
and WO 93/15187; European Patent Application No. 92110298.4;
Perrault et al., Nature, 344:565 (1990); Pieken et al., Science,
253:314 (1991); and Usman and Cedergren, Trends in Biochem. Sci.,
17:334 (1992).
[0221] Ribozymes of the present invention may be administered to
cells by any known methods, e.g., disclosed in International
Publication No. WO 94/02595. For example, they can be administered
directly to cells or tissue in vitro or in a patient through any
suitable route, e.g., intravenous injection. Alternatively, they
may be delivered encapsulated in liposomes, by iontophoresis, or by
incorporation into other vehicles such as hydrogels, cyclodextrins,
biodegradable nanocapsules, and bioadhesive microspheres. In
addition, they may also be delivered by gene therapy approach,
using a DNA vector from which the ribozyme RNA can be transcribed
directly. Gene therapy methods are disclosed in detail below in
Section 6.3.2.
6.2.4. Other Methods
[0222] The in-patient concentrations and activities of the protein
complexes and interacting proteins of the present invention may
also be altered by other methods. For example, compounds identified
in accordance with the methods described in Section 5 that are
capable of interfering with or dissociating protein-protein
interactions between the interacting protein members of a protein
complex may be administered to cells or tissue in vitro or in a
patient. Compounds identified in in vitro binding assays described
in Section 5.2 that bind to the APOA1-containing protein complex or
the interacting members thereof may also be used in the treatment.
Compounds identified in in vitro binding assays described in
Section 5.2 that bind to the APOA1-containing protein complex, or
the interacting members thereof, may also be used in the treatment.
In addition, potentially useful agents also include incomplete
proteins, i.e., fragments of the interacting protein members that
are capable of binding to their respective binding partners in a
protein complex but are defective with respect to their normal
cellular functions. For example, binding domains of the interacting
member proteins of a protein complex may be used as competitive
inhibitors of the activities of the protein complex. As will be
apparent to skilled artisans, derivatives or homologues of the
binding domains may also be used. Binding domains can be easily
identified using molecular biology techniques, e.g., mutagenesis in
combination with yeast two-hybrid assays. Preferably, the protein
fragment used is a fragment of an interacting protein member having
a length of less than 90%, 80%, more preferably less than 75%, 65%,
50%, or less than 40% of the full length of the protein member. In
one embodiment, an APOA1 protein fragment is administered. In a
specific embodiment, one or more of the interaction domains of
APOA1 within the regions listed in Table 1 are administered to
cells or tissue in vitro, or are administered to a patient in need
of such treatment. For example, suitable protein fragments can
include polypeptides having a contiguous span of 4, 5, 6, 7, 8, 9,
10, 11, 12, 13, 14, 15, 18, 20 or 25, preferably from 4 to 30, 40
or 50 amino acids or more of the sequence of APOA1 that are capable
of interacting with one or more proteins selected from the group of
PRA1, GOLGIN-84, Syntaxin 2, APOB and FLJ20724. Also, suitable
protein fragments can also include peptides capable of binding one
or more proteins selected from the group of PRA1, GOLGIN-84,
Syntaxin 2, APOB and FLJ20724 and having an amino acid sequence of
from 4 to 30 amino acids that is at least 75%, 80%, 82%, 85%, 87%,
90%, 95% or more identical to a contiguous span of amino acids of
APOA1 of the same length. Alternatively, a polypeptide capable of
interacting with APOA1 and having a contiguous span of 4, 5, 6, 7,
8, 9, 10, 11, 12, 13, 14, 15, 18, 20 or 25, preferably from 4 to
30, 40 or 50 or more amino acids of the amino acid sequence of a
protein selected from the group of PRA1, GOLGIN-84, Syntaxin 2,
APOB and FLJ20724 may be administered. Also, other examples of
suitable compounds include a peptide capable of binding APOA1 and
having an amino acid sequence of from 4 to 30, 40, 50 or more amino
acids that is at least 75%, 80%, 82%, 85%, 87%, 90%, 92%, 95% or
more identical to a contiguous span of amino acids of the same
length from a protein selected from the group of PRA1, GOLGIN-84,
Syntaxin 2, APOB and FLJ20724. In addition, the administered
compounds can be an antibody or antibody fragment, preferably
single-chain antibody immunoreactive with APOA1 or a protein
selected from the group of PRA1, GOLGIN-84, Syntaxin 2, APOB and
FLJ20724, or a protein complex of the present invention.
[0223] The protein fragments suitable as competitive inhibitors can
be delivered into cells by direct cell internalization, receptor
mediated endocytosis, or via a "transporter."
[0224] It is noted that when the target proteins or protein
complexes to be modulated reside inside cells, the compound
administered to cells in vitro or in vivo in the method of the
present invention preferably is delivered into the cells in order
to achieve optimal results. Thus, preferably, the compound to be
delivered is associated with a transporter capable of increasing
the uptake of the compound by cells harboring the target protein or
protein complex. As used herein, the term "transporter" refers to
an entity (e.g., a compound or a composition or a physical
structure formed from multiple copies of a compound or multiple
different compounds) that is capable of facilitating the uptake of
a compound of the present invention by animal cells, particularly
human cells. Typically, the cell uptake of a compound of the
present invention in the presence of a "transporter" is at least
20% higher, preferably at least 40%, 50%, 75%, and more preferably
at least 100% higher than the cell uptake of the compound in the
absence of the "transporter."
[0225] Many molecules and structures known in the art can be used
as "transporters." In one embodiment, a penetratin is used as a
transporter. For example, the homeodomain of Antennapedia, a
Drosophila transcription factor, can be used as a transporter to
deliver a compound of the present invention. Indeed, any suitable
member of the penetratin class of peptides can be used to carry a
compound of the present invention into cells. Penetratins are
disclosed in, e.g., Derossi et al., Trends Cell Biol., 8:84-87
(1998), which is incorporated herein by reference. Penetratins
transport molecules attached thereto across cytoplasmic membranes
or nuclear membranes efficiently, in a receptor-independent,
energy-independent, and cell type-independent manner. Methods for
using a penetratin as a carrier to deliver oligonucleotides and
polypeptides are also disclosed in U.S. Pat. No. 6,080,724; Pooga
et al., Nat. Biotech., 16:857 (1998); and Schutze et al., J.
Immunol., 157:650 (1996), all of which are incorporated herein by
reference. U.S. Pat. No. 6,080,724 defines the minimal requirements
for a penetratin peptide as a peptide of 16 amino acids with 6 to
10 of which being hydrophobic. The amino acid at position 6
counting from either the N- or C-terminus is tryptophan, while the
amino acids at positions 3 and 5 counting from either the N- or
C-terminus are not both valine. Preferably, the helix 3 of the
homeodomain of Drosophila Antennapedia is used as a transporter.
More preferably, a peptide having a sequence of amino acid residues
43-58 of the homeodomain Antp is employed as a transporter. In
addition, other naturally occurring homologs of the helix 3 of the
homeodomain of Drosophila Antennapedia can be used. For example,
homeodomains of Fushi-tarazu and Engrailed have been shown to be
capable of transporting peptides into cells. See Han et al., Mol.
Cells, 10:728-32 (2000). As used herein, the term "penetratin" also
encompasses peptoid analogs of the penetratin peptides. Typically,
the penetratin peptides and peptoid analogs thereof are covalently
linked to a compound to be delivered into cells thus increasing the
cellular uptake of the compound.
[0226] In another embodiment, the HIV-1 tat protein or a derivative
thereof is used as a "transporter" covalently linked to a compound
according to the present invention. The use of UV-1 tat protein and
derivatives thereof to deliver macromolecules into cells has been
known in the art. See Green and Loewenstein, Cell, 55:1179 (1988);
Frankel and Pabo, Cell, 55:1189 (1988); Vives et al., J. Biol.
Chem., 272:16010-16017 (1997); Schwarze et al., Science,
285:1569-1572 (1999). It is known that the sequence responsible for
cellular uptake consists of the highly basic region, amino acid
residues 49-57. See e.g., Vives et al., J. Biol. Chem.,
272:16010-16017 (1997); Wender et al., Proc. Nat'l. Acad. Sci. USA,
97:13003-13008 (2000). The basic domain is believed to target the
lipid bilayer component of cell membranes. It causes a covalently
linked protein or nucleic acid to cross cell membrane rapidly in a
cell type-independent manner. Proteins ranging in size from 15 to
120 kD have been delivered with this technology into a variety of
cell types both in vitro and in vivo. See Schwarze et al., Science,
285:1569-1572 (1999). Any HIV tat-derived peptides or peptoid
analogs thereof capable of transporting macromolecules such as
peptides can be used for purposes of the present invention. For
example, any native tat peptides having the highly basic region,
amino acid residues 49-57 can be used as a transporter by
covalently linking it to the compound to be delivered. In addition,
various analogs of the tat peptide of amino acid residues 49-57 can
also be useful transporters for purposes of this invention.
Examples of various such analogs are disclosed in Wender et al.,
Proc. Nat'l Acad. Sci. USA, 97:13003-13008 (2000) (which is
incorporated herein by reference) including, e.g., d-Tat.sub.49-57,
retro-inverso isomers of L- or d-Tat.sub.49-57 (i.e.,
l-Tat.sub.57-49 and d-Tat.sub.57-49), L-arginine oligomers,
D-arginine oligomers, L-lysine oligomers, D-lysine oligomers,
L-histine oligomers, D-histine oligomers, L-omithine oligomers,
D-omithine oligomers, and various homologues, derivatives (e.g.,
modified forms with conjugates linked to the small peptides) and
peptoid analogs thereof.
[0227] Other useful transporters known in the art include, but are
not limited to, short peptide sequences derived from fibroblast
growth factor (See Lin et al., J. Biol. Chem., 270:14255-14258
(1998)), Galparan (See Pooga et al., FASEB J. 12:67-77 (1998)), and
HSV-1 structural protein VP22 (See Elliott and O'Hare, Cell,
88:223-233 (1997)).
[0228] As the above-described various transporters are generally
peptides, fusion proteins can be conveniently made by recombinant
expression to contain a transporter peptide covalently linked by a
peptide bond to a competitive protein fragment. Alternatively,
conventional methods can be used to chemically synthesize a
transporter peptide or a peptide of the present invention or
both.
[0229] The hybrid peptide can be administered to cells or tissue in
vitro or to a patient in a suitable pharmaceutical composition as
provided in Section 8.
[0230] In addition to peptide-based transporters, various other
types of transporters can also be used, including but not limited
to cationic liposomes (see Rui et al., J. Am. Chem. Soc.,
120:11213-11218 (1998)), dendrimers (Kono et al., Bioconjugate
Chem., 10:1115-1121 (1999)), siderophores (Ghosh et al., Chem.
Biol., 3:1011-1019 (1996)), etc. In a specific embodiment, the
compound according to the present invention is encapsulated into
liposomes for delivery into cells.
[0231] Additionally, when a compound according to the present
invention is a peptide, it can be administered to cells by a gene
therapy method. That is, a nucleic acid encoding the peptide can be
administered to in vitro cells or to cells in vivo in a human or
animal body. Any suitable gene therapy methods may be used for
purposes of the present invention. Various gene therapy methods are
well known in the art and are described in Section 6.3.2. below.
Successes in gene therapy have been reported recently. See e.g.,
Kay et al., Nature Genet., 24:257-61 (2000); Cavazzana-Calvo et
al., Science, 288:669 (2000); and Blaese et al., Science, 270: 475
(1995); Kantoff, et al., J. Exp. Med., 166:219 (1987).
[0232] In yet another embodiment, the gene therapy methods
discussed in Section 6.3.2 below are used to "knock out" the gene
encoding an interacting protein member of a protein complex, or to
reduce the gene expression level. For example, the gene may be
replaced with a different gene sequence or a non-functional
sequence or simply deleted by homologous recombination. In another
gene therapy embodiment, the method disclosed in U.S. Pat. No.
5,641,670, which is incorporated herein by reference, may be used
to reduce the expression of the genes for the interacting protein
members. Essentially, an exogenous DNA having at least a regulatory
sequence, an exon and a splice donor site can be introduced into an
endogenous gene encoding an interacting protein member by
homologous recombination such that the regulatory sequence, the
exon and the splice donor site present in the DNA construct become
operatively linked to the endogenous gene. As a result, the
expression of the endogenous gene is controlled by the newly
introduced exogenous regulatory sequence. Therefore, when the
exogenous regulatory sequence is a strong gene expression
repressor, the expression of the endogenous gene encoding the
interacting protein member is reduced or blocked. See U.S. Pat. No.
5,641,670.
6.3. Activation of Protein Complex or Interacting Protein Members
Thereof
[0233] The present invention also provides methods for increasing
in cells or tissue in vitro or in a patient the concentration
and/or activity of a protein complex, or of an individual protein
member thereof, identified in accordance with the present
invention. Such methods can be particularly useful in instances
where a reduced concentration and/or activity of a protein complex,
or a protein member thereof, is associated with a particular
disease or disorder to be treated, or where an increased
concentration and/or activity of a protein complex, or a protein
member thereof, would be beneficial to the improvement of a
cellular function or disease state. By increasing the concentration
of the protein complex, or a protein member thereof, and/or
stimulating the functional activities of the protein complex or a
protein member thereof, the disease or disorder may be treated or
prevented.
6.3.1. Administration of Protein Complex or Protein Members
Thereof
[0234] Where the concentration or activity of a particular
APOA11-containing protein complex, or APOA1 itself, or an
APOA1-interacting protein of the present invention, in cells or
tissue in vitro or in a patient is determined to be low or is
desired to be increased, the protein complex, or APOA1, or the
APOA1-interacting protein may be administered directly to the
patient to increase the concentration and/or activity of the
protein complex, APOA1, or the APOA1-interacting protein. For this
purpose, protein complexes prepared by any one of the methods
described in Section 2.2 may be administered to the patient,
preferably in a pharmaceutical composition as described below.
Alternatively, one or more individual interacting protein members
of the protein complex may also be administered to the patient in
need of treatment. For example, one or more proteins such as APOA1,
PRA1, GOLGIN-84, Syntaxin 2, APOB and FLJ20724 may be given to
cells or tissue in vitro or to a patient. Proteins isolated or
purified from normal individuals or recombinantly produced can all
be used in this respect. Preferably, two or more interacting
protein members of a protein complex are administered. The proteins
or protein complexes may be administered to a patient needing
treatment using any of the methods described in Section 8.
6.3.2. Gene Therapy
[0235] In another embodiment, the concentration and/or activity of
a particular APOA1-containing protein complex or APOA1, or a known
APOA1 -interacting protein (selected from the group including PRA1,
GOLGIN-84, Syntaxin 2, APOB and FLJ20724) is increased or restored
in patients, tissue or cells by a gene therapy approach. For
example, nucleic acids encoding one or more protein members of an
APOA1-containing protein complex of the present invention, or
portions or fragments thereof are introduced into patients, tissue,
or cells such that the protein(s) are expressed from the introduced
nucleic acids. For these purposes, nucleic acids encoding one or
more of APOA1, PRA1, GOLGIN-84, Syntaxin 2, APOB and FLJ20724, or
fragments, homologues or derivatives thereof can be used in the
gene therapy in accordance with the present invention. For example,
if a disease-causing mutation exists in one of the protein members
in cells or tissue in vitro or in a patient, then a nucleic acid
encoding a wild-type protein can be introduced into tissue cells of
the patient. The exogenous nucleic acid can be used to replace the
corresponding endogenous defective gene by, e.g., homologous
recombination. See U.S. Pat. No. 6,010,908, which is incorporated
herein by reference. Alternatively, if the disease-causing mutation
is a recessive mutation, the exogenous nucleic acid is simply used
to express a wild-type protein in addition to the endogenous mutant
protein. In another approach, the method disclosed in U.S. Pat. No.
6,077,705 may be employed in gene therapy. That is, the patient is
administered both a nucleic acid construct encoding a ribozyme and
a nucleic acid construct comprising a ribozyme resistant gene
encoding a wild type form of the gene product. As a result,
undesirable expression of the endogenous gene is inhibited and a
desirable wild-type exogenous gene is introduced. In yet another
embodiment, if the endogenous gene is of wild-type and the level of
expression of the protein encoded thereby is desired to be
increased, additional copies of wild-type exogenous genes may be
introduced into the patient by gene therapy, or alternatively, a
gene activation method such as that disclosed in U.S. Pat. No.
5,641,670 may be used.
[0236] Various gene therapy methods are well known in the art.
Successes in gene therapy have been reported recently. See e.g.,
Kay et al., Nature Genet., 24:257-61 (2000); Cavazzana-Calvo et
al., Science, 288:669 (2000); and Blaese et al., Science, 270: 475
(1995); Kantoff, et al., J. Exp. Med. 166:219 (1987).
[0237] Any suitable gene therapy methods may be used for the
purposes of the present invention. Generally, a nucleic acid
encoding a desirable protein (e.g., one selected from APOA1, PRA1,
GOLGIN-84, Syntaxin 2, APOB and FLJ20724) is incorporated into a
suitable expression vector and is operably linked to a promoter in
the vector. Suitable promoters include but are not limited to viral
transcription promoters derived from adenovirus, simian virus 40
(SV40) (e.g., the early and late promoters of SV40), Rous sarcoma
virus (RSV), and cytomegalovirus (CMV) (e.g., CMV immediate-early
promoter), human immunodeficiency virus (HIV) (e.g., long terminal
repeat (LTR)), vaccinia virus (e.g., 7.5K promoter), and herpes
simplex virus (HSV) (e.g., thymidine kinase promoter). Where
tissue-specific expression of the exogenous gene is desirable,
tissue-specific promoters may be operably linked to the exogenous
gene. In addition, selection markers may also be included in the
vector for purposes of selecting, in vitro, those cells that
contain the exogenous gene. Various selection markers known in the
art may be used including, but not limited to, e.g., genes
conferring resistance to neomycin, hygromycin, zeocin, and the
like.
[0238] In one embodiment, the exogenous nucleic acid (gene) is
incorporated into a plasmid DNA vector. Many commercially available
expression vectors may be useful for the present invention,
including, e.g., pCEP4, pcDNAI, pIND, pSecTag2, pVAX1, pcDNA3.1,
and pBI-EGFP, and pDisplay.
[0239] Various viral vectors may also be used. Typically, in a
viral vector, the viral genome is engineered to eliminate the
disease-causing capability of the virus, e.g., the ability to
replicate in the host cells. The exogenous nucleic acid to be
introduced into cells or tissue in vitro or in a patient may be
incorporated into the engineered viral genome, e.g., by inserting
it into a viral gene that is non-essential to the viral
infectivity. Viral vectors are convenient to use as they can be
easily introduced into cells, tissues and patients by way of
infection. Once in the host cell, the recombinant virus typically
is integrated into the genome of the host cell. In rare instances,
the recombinant virus may also replicate and remain as
extrachromosomal elements.
[0240] A large number of retroviral vectors have been developed for
gene therapy. These include vectors derived from oncoretroviruses
(e.g., MLV), lentiviruses (e.g., HIV and SIV) and other
retroviruses. For example, gene therapy vectors have been developed
based on murine leukemia virus (See, Cepko, et al., Cell,
37:1053-1062 (1984), Cone and Mulligan, Proc. Natl. Acad. Sci.
U.S.A., 81:6349-6353 (1984)), mouse mammary tumor virus (See,
Salmons et al., Biochem. Biophys. Res. Commun., 159:1191-1198
(1984)), gibbon ape leukemia virus (See, Miller et al., J.
Virology, 65:2220-2224 (1991)), HIV, (See Shimada et al., J. Clin.
Invest., 88:1043-1047 (1991)), and avian retroviruses (See Cosset
et al., J. Virology, 64:1070-1078 (1990)). In addition, various
retroviral vectors are also described in U.S. Pat. Nos. 6,168,916;
6,140,111; 6,096,534; 5,985,655; 5,911,983; 4,980,286; and
4,868,116, all of which are incorporated herein by reference.
[0241] Adeno-associated virus (AAV) vectors have been successfully
tested in clinical trials. See e.g., Kay et al., Nature Genet.
24:257-61 (2000). AAV is a naturally occurring defective virus that
requires other viruses such as adenoviruses or herpes viruses as
helper viruses. See Muzyczka, Curr. Top. Microbiol. Immun., 158:97
(1992). A recombinant AAV virus useful as a gene therapy vector is
disclosed in U.S. Pat. No. 6,153,436, which is incorporated herein
by reference.
[0242] Adenoviral vectors can also be useful for purposes of gene
therapy in accordance with the present invention. For example, U.S.
Pat. No. 6,001,816 discloses an adenoviral, which is used to
deliver a leptin gene intravenously to a mammal to treat obesity.
Other recombinant adenoviral vectors may also be used, which
include those disclosed in U.S. Pat. Nos. 6,171,855; 6,140,087;
6,063,622; 6,033,908; and 5,932,210, and Rosenfeld et al., Science,
252:431-434 (1991); and Rosenfeld et al., Cell, 68:143-155
(1992).
[0243] Other useful viral vectors include recombinant hepatitis
viral vectors (See, e.g., U.S. Pat. No. 5,981,274), and recombinant
entomopox vectors (See, e.g., U.S. Pat. Nos. 5,721,352 and
5,753,258).
[0244] Other non-traditional vectors may also be used for purposes
of this invention. For example, International Publication No. WO
94/18834 discloses a method of delivering DNA into mammalian cells
by conjugating the DNA to be delivered with a polyelectrolyte to
form a complex. The complex may be microinjected into or taken up
by cells.
[0245] The exogenous gene fragment or plasmid DNA vector containing
the exogenous gene may also be introduced into cells by way of
receptor-mediated endocytosis. See e.g., U.S. Pat. No. 6,090,619;
Wu and Wu, J. Biol. Chem., 263:14621 (1988); Curiel et al., Proc.
Natl. Acad. Sci. USA, 88:8850 (1991). For example, U.S. Pat. No.
6,083,741 discloses introducing an exogenous nucleic acid into
mammalian cells by associating the nucleic acid to a polycation
moiety (e.g., poly-L-lysine having 3-100 lysine residues), which is
itself coupled to an integrin receptor binding moiety (e.g., a
cyclic peptide having the sequence Arg-Gly-Asp).
[0246] Alternatively, the exogenous nucleic acid or vectors
containing it can also be delivered into cells via amphiphiles. See
e.g., U.S. Pat. No. 6,071,890. Typically, the exogenous nucleic
acid or a vector containing the nucleic acid forms a complex with
the cationic amphiphile. Mammalian cells contacted with the complex
can readily take it up.
[0247] The exogenous gene can be introduced into cells or tissue in
vitro or in a patient for purposes of gene therapy by various
methods known in the art. For example, the exogenous gene sequences
alone or in a conjugated or complex form described above, or
incorporated into viral or DNA vectors, may be administered
directly by injection into an appropriate tissue or organ of a
patient. Alternatively, catheters or like devices may be used to
deliver exogenous gene sequences, complexes, or vectors into a
target organ or tissue. Suitable catheters are disclosed in, e.g.,
U.S. Pat. Nos. 4,186,745; 5,397,307; 5,547,472; 5,674,192; and
6,129,705, all of which are incorporated herein by reference.
[0248] In addition, the exogenous gene or vectors containing the
gene can be introduced into isolated cells using any known
techniques such as calcium phosphate precipitation, microinjection,
lipofection, electroporation, biolystics, receptor-mediated
endocytosis, and the like. Cells expressing the exogenous gene may
be selected and redelivered back to the patient by, e.g., injection
or cell transplantation. The appropriate amount of cells delivered
to a patient will vary with patient conditions, and desired effect,
which can be determined by a skilled artisan. See e.g., U.S. Pat.
Nos. 6,054,288; 6,048,524; and 6,048,729. Preferably, the cells
used are autologous, i.e., cells obtained from the patient being
treated.
6.3.3. Small Organic Compounds
[0249] Defective conditions or disorders in cells or tissue in
vitro or in a patient associated with decreased concentration or
activity of an APOA1-containing protein complex, APOA1, or an
APOA1-interacting protein identified in accordance with the present
invention, can also be ameliorated by administering to the patient
a compound identified by the methods described in Sections 5.3.1.4,
5.2, and Section 5.4, which is capable of modulating the functions
of the protein complex or the APOA1-interacting protein, e.g., by
triggering or initiating, enhancing or stabilizing protein-protein
interaction between the interacting protein members of the protein
complex, or the mutant forms of such interacting protein members
found in the patient.
7. Cell and Animal Models
[0250] In another aspect of the present invention, cell and animal
models are provided in which one or more of the APOA1 -containing
protein complexes identified in the present invention, or APOA1
itself, or a member, or members of the group consisting of PRA1,
GOLGIN-84, Syntaxin 2, APOB and FLJ20724, exhibit aberrant
function, activity, or concentration when compared with wildtype
cells and animals (e.g., increased or decreased concentration,
altered interactions between protein complex constituents due to
mutations in interaction domains, and/or altered distribution or
localization of the protein complexes or constituents thereof in
organs, tissues, cells, or cellular compartments). Such cell and
animal models are useful tools for studying cellular functions and
biological processes associated with the protein complexes of the
present invention, or with APOA1 itself, or with an
APOA1-interacting protein identified in accordance with the present
invention. Such cell and animal models are also useful tools for
studying disorders and diseases associated with the protein
complexes of the present invention, or APOA1 itself, or a member,
or members of the group PRA1, GOLGIN-84, Syntaxin 2, APOB and
FLJ20724, and for testing various methods for modulating the
cellular functions, and for treating the diseases and disorders,
associated with aberrations in these protein complexes or the
protein constituents thereof.
7.1. Cell Models
[0251] Cell models having an aberrant form of one or more of the
protein complexes of the present invention are provided in
accordance with the present invention.
[0252] The cell models may be established by isolating, from a
patient, cells having an aberrant form of one or more of the
protein complexes of the present invention. The isolated cells may
be cultured in vitro as a primary cell culture. Alternatively, the
cells obtained from the primary cell culture or directly from the
patient may be immortalized to establish a human cell line. Any
methods for constructing immortalized human cell lines may be used
in this respect. See generally Yeager and Reddel, Curr. Opini.
Biotech., 10:465-469 (1999). For example, the human cells may be
immortalized by transfection of plasmids expressing the SV40 early
region genes (See e.g., Jha et al., Exp. Cell Res., 245:1-7
(1998)), introduction of the HPV E6 and E7 oncogenes (See e.g.,
Reznikoff et al., Genes Dev., 8:2227-2240 (1994)), and infection
with Epstein-Barr virus (See e.g., Tahara et al., Oncogene,
15:1911-1920 (1997)). Alternatively, the human cells may be
immortalized by recombinantly expressing the gene for the human
telomerase catalytic subunit hTERT in the human cells. See Bodnar
et al., Science, 279:349-352 (1998).
[0253] In alternative embodiments, cell models are provided by
recombinantly manipulating appropriate host cells. The host cells
may be bacteria cells, yeast cells, insect cells, plant cells,
animal cells, and the like. Preferably, the cells are derived from
mammals, most preferably humans. The host cells may be obtained
directly from an individual, or a primary cell culture, or
preferably an immortal stable human cell line. In a preferred
embodiment, human embryonic stem cells or pluripotent cell lines
derived from human stem cells are used as host cells. Methods for
obtaining such cells are disclosed in, e.g., Shamblott, et al.,
Proc. Natl. Acad. Sci. USA, 95:13726-13731 (1998) and Thomson et
al., Science, 282:1145-1147 (1998).
[0254] In one embodiment, a cell model is provided by recombinantly
expressing one or more of the protein complexes of the present
invention in cells that do not normally express such protein
complexes. For example, cells that do not contain a particular
protein complex may be engineered to express the protein complex.
In a specific embodiment, a particular human protein complex is
expressed in non-human cells. The cell model may be prepared by
introducing into host cells nucleic acids encoding all interacting
protein members required for the formation of a particular protein
complex, and expressing the protein members in the host cells. For
this purpose, the recombinant expression methods described in
Section 2.2 may be used. In addition, the methods for introducing
nucleic acids into host cells disclosed in the context of gene
therapy in Section 6.2.2 may also be used.
[0255] In another embodiment, a cell model over-expressing one or
more of the protein complexes of the present invention is provided.
The cell model may be established by increasing the expression
level of one or more of the interacting protein members of the
protein complexes. In a specific embodiment, all interacting
protein members of a particular protein complex are over-expressed.
The over-expression may be achieved by introducing into host cells
exogenous nucleic acids encoding the proteins to be over-expressed,
and selecting those cells that over-express the proteins. The
expression of the exogenous nucleic acids may be transient or,
preferably stable. The recombinant expression methods described in
Section 2.2, and the methods for introducing nucleic acids into
host cells disclosed in the context of gene therapy in Section
6.2.2 may be used. Alternatively, the gene activation method
disclosed in U.S. Pat. No. 5,641,670 can be used. Any host cells
may be employed for establishing the cell model. Preferably, human
cells lacking a protein complex to be over-expressed, or having a
normal concentration of the protein complex, are used as host
cells. The host cells may be obtained directly from an individual,
or a primary cell culture, or preferably a stable immortal human
cell line. In a preferred embodiment, human embryonic stem cells or
pluripotent cell lines derived from human stem cells are used as
host cells. Methods for obtaining such cells are disclosed in,
e.g., Shamblott, et al., Proc. Natl. Acad. Sci. USA, 95:13726-13731
(1998), and Thomson et al., Science, 282:1145-1147 (1998).
[0256] In yet another embodiment, a cell model expressing an
abnormally low level of one or more of the protein complexes of the
present invention is provided. Typically, the cell model is
established by genetically manipulating cells that express a normal
and detectable level of a protein complex identified in accordance
with the present invention. Generally the expression level of one
or more of the interacting protein members of the protein complex
is reduced by recombinant methods. In a specific embodiment, the
expression of all interacting protein members of a particular
protein complex is reduced. The reduced expression may be achieved
by "knocking out" the genes encoding one or more interacting
protein members. Alternatively, mutations that can cause reduced
expression level (e.g., reduced transcription and/or translation
efficiency, and decreased mRNA stability) may also be introduced
into the gene by homologous recombination. A gene encoding a
ribozyme or antisense compound specific to the mRNA encoding an
interacting protein member may also be introduced into the host
cells, preferably stably integrated into the genome of the host
cells. In addition, a gene encoding an antibody or fragment thereof
specific to an interacting protein member may also be introduced
into the host cells. The recombinant expression methods described
in Sections 2.2, 6.1 and 6.2 can all be used for purposes of
manipulating the host cells.
[0257] The present invention also contemplates a cell model
provided by recombinant DNA techniques that exhibits aberrant
interactions between the interacting protein members of a protein
complex identified in the present invention. For example, variants
of the interacting protein members of a particular protein complex
exhibiting altered protein-protein interaction properties and the
nucleic acid variants encoding such variant proteins may be
obtained by random or site-directed mutagenesis in combination with
a protein-protein interaction assay system, particularly the yeast
two-hybrid system described in Section 5.3.1. Essentially, the
genes encoding one or more interacting protein members of a
particular protein complex may be subject to random or
site-specific mutagenesis and the mutated gene sequences are used
in yeast two-hybrid system to test the protein-protein interaction
characteristics of the protein variants encoded by the gene
variants. In this manner, variants of the interacting protein
members of the protein complex may be identified that exhibit
altered protein-protein interaction properties in forming the
protein complex, e.g., increased or decreased binding affinity, and
the like. The nucleic acid variants encoding such protein variants
may be introduced into host cells by the methods described above,
preferably into host cells that normally do not express the
interacting proteins.
7.2. Cell-Based Assays
[0258] The cell models of the present invention containing an
aberrant form of an APOA1 -containing protein complex of the
present invention are useful in screening assays for identifying
compounds useful in treating diseases and disorders involving
cholesterol transport and lipid metabolism such as dementia such as
Alzheimer's disease and cardiovascular diseases such as coronary
heart disease, atherosclerosis, hypercholesterolemia, Tangier
disease and amyloidosis. In addition, they may also be used in in
vitro pre-clinical assays for testing compounds, such as those
identified in the screening assays of the present invention.
[0259] For example, cells may be treated with compounds to be
tested and assayed for the compound's activity. A variety of
parameters relevant to particularly physiological disorders or
diseases may be analyzed.
7.3. Transgenic Animals
[0260] In another aspect of the present invention, transgenic
non-human animals are created expressing an aberrant form of one or
more of the APOA1-containing protein complexes of the present
invention. Animals of any species may be used to generate the
transgenic animal models, including but not limited to, mice, rats,
hamsters, sheep, pigs, rabbits, guinea pigs, preferably non-human
primates such as monkeys, chimpanzees, baboons, and the like.
[0261] In one embodiment, transgenic animals are made to
over-express one or more protein complexes formed from APOA1, or a
derivative, fragment or homologue thereof (including the animal
counterpart of APOA1, i.e., an orthologue) and a member, or
members, of the group of APOA1-interacting proteins including PRA1,
GOLGIN-84, Syntaxin 2, APOB and FLJ20724, or derivatives, fragments
or homologues thereof (including orthologues). Over-expression may
be directed in a tissue or cell type that normally expresses animal
counterparts of such protein complexes. Consequently, the
concentration of the protein complex(es) will be elevated to higher
levels than normal. Alternatively, the one or more protein
complexes are expressed in tissues or cells that do not normally
express such proteins and hence do not normally contain the protein
complexes of the present invention. In a specific embodiment, human
APOA1 and a human protein, or proteins, from the group of
APOA1-interacting proteins including PRA1, GOLGIN-84, Syntaxin 2,
APOB and FLJ20724, are expressed in the transgenic animals.
[0262] To achieve over-expression in transgenic animals, the
transgenic animals are made such that they contain and express
exogenous, orthologous genes encoding APOA1or a homologue,
derivative or mutant form thereof and one or more APOA1-interacting
proteins or homologues, derivatives or mutant forms thereof.
Preferably, the exogenous genes are human genes. Such exogenous
genes may be operably linked to a native or non-native promoter,
preferably a non-native promoter. For example, an exogenous APOA1
gene may be operably linked to a promoter that is not the native
APOA1promoter. If the expression of the exogenous gene is desired
to be limited to a particular tissue, an appropriate
tissue-specific promoter may be used.
[0263] Over-expression may also be achieved by manipulating the
native promoter to create mutations that lead to gene
over-expression, or by a gene activation method such as that
disclosed in U.S. Pat. No. 5,641,670 as described above.
[0264] In another embodiment, the transgenic animal expresses an
abnormally low concentration of the complex comprising APOA1 and
one or more of the APOA1-interacting proteins from the group PRA1,
GOLGIN-84, Syntaxin 2, APOB and FLJ20724. In a specific embodiment,
the transgenic animal is a "knockout" animal wherein the endogenous
gene encoding the animal orthologue of APOA1 and/or an endogenous
gene encoding an animal orthologue of an APOA1-interacting protein
are knocked out. In a specific embodiment, the expression of the
animal orthologues of both APOA1 and an APOA1-interacting protein,
or proteins, from the group PRA1, GOLGIN-84, Syntaxin 2, APOB and
FLJ20724 are reduced or knocked out. The reduced expression may be
achieved by knocking out the genes encoding one or both interacting
protein members, typically by homologous recombination.
Alternatively, mutations that can cause reduced expression (e.g.,
reduced transcription and/or translation efficiency, or decreased
mRNA stability) may also be introduced into the endogenous genes by
homologous recombination. Genes encoding ribozymes or antisense
compounds specific to the mRNAs encoding the interacting protein
members may also be introduced into the transgenic animal. In
addition, genes encoding antibodies or fragments thereof specific
to the interacting protein members may also be introduced into the
transgenic animal.
[0265] In an alternate embodiment, transgenic animals are made in
which the endogenous genes encoding the animal orthologues of APOA1
and one or more APOA1-interacting proteins from the group PRA1,
GOLGIN-84, Syntaxin 2, APOB and FLJ20724 are replaced with
orthologous human genes.
[0266] In yet another embodiment, the transgenic animal of this
invention expresses specific mutant forms of APOA1 and one or more
APOA1-interacting proteins from the group PRA1, GOLGIN-84, Syntaxin
2, APOB and FLJ20724 that exhibit aberrant interactions. For this
purpose, variants of APOA1 and one or more APOA1-interacting
proteins from the group PRA1, GOLGIN-84, Syntaxin 2, APOB and
FLJ20724 exhibiting altered protein-protein interaction properties,
and the nucleic acid variants encoding such variant proteins, may
be obtained by random or site-specific mutagenesis in combination
with a protein-protein interaction assay system, particularly the
yeast two-hybrid system described in Section 5.3.1. For example,
variants of APOA1 and PRA1exhibiting increased, decreased or
abolished binding affinity to each other may be identified and
isolated. The transgenic animal of the present invention may be
made to express such protein variants by modifying the endogenous
genes. Alternatively, the nucleic acid variants may be introduced
exogenously into the transgenic animal genome to express the
protein variants therein. In a specific embodiment, the exogenous
nucleic acid variants are derived from orthologous human genes and
the corresponding endogenous genes are knocked out.
[0267] Any techniques known in the art for making transgenic
animals may be used for purposes of the present invention. For
example, the transgenic animals of the present invention may be
provided by methods described in, e.g., Jaenisch, Science, 240:1468
1474 (1988); Capecchi, et al., Science, 244:1288-1291 (1989); Hasty
et al., Nature, 350:243 (1991); Shinkai et al., Cell, 68:855
(1992); Mombaerts et al., Cell, 68:869 (1992); Philpott et al.,
Science, 256:1448 (1992); Snouwaert et al., Science, 257:1083
(1992); Donehower et al., Nature, 356:215 (1992); Hogan et al.,
Manipulating the Mouse Embryo; A Laboratory Manual, 2.sup.nd
edition, Cold Spring Harbor Laboratory Press, 1994; and U.S. Pat.
Nos. 4,873,191; 5,800,998; 5,891,628, all of which are incorporated
herein by reference.
[0268] Generally, the founder lines may be established by
introducing appropriate exogenous nucleic acids into, or modifying
an endogenous gene in, germ lines, embryonic stem cells, embryos,
or sperm which are then used in producing a transgenic animal. The
gene introduction may be conducted by various methods including
those described in Sections 2.2, 6.1 and 6.2. See also, Van der
Putten et al., Proc. Natl. Acad. Sci. USA, 82:6148-6152 (1985);
Thompson et al., Cell, 56:313-321 (1989); Lo, Mol. Cell. Biol.,
3:1803-1814 (1983); Gordon, Trangenic Animals, Intl. Rev. Cytol.
115:171-229 (1989); and Lavitrano et al., Cell, 57:717-723 (1989).
In a specific embodiment, the exogenous gene is incorporated into
an appropriate vector, such as those described in Sections 2.2 and
6.2, and is transformed into embryonic stem (ES) cells. The
transformed ES cells are then injected into a blastocyst. The
blastocyst with the transformed ES cells is then implanted into a
surrogate mother animal. In this manner, a chimeric founder line
animal containing the exogenous nucleic acid (transgene) may be
produced.
[0269] Preferably, site-specific recombination is employed to
integrate the exogenous gene into a specific predetermined site in
the animal genome, or to replace an endogenous gene or a portion
thereof with the exogenous sequence. Various site-specific
recombination systems may be used including those disclosed in
Sauer, Curr. Opin. Biotechnol., 5:521-527 (1994); Capecchi, et al.,
Science, 244:1288-1291 (1989); and Gu et al., Science, 265:103-106
(1994). Specifically, the Cre/lox site-specific recombination
system known in the art may be conveniently used which employs the
bacteriophage P1 protein Cre recombinase and its recognition
sequence loxP. See Rajewsky et al., J. Clin. Invest., 98:600-603
(1996); Sauer, Methods, 14:381-392 (1998); Gu et al., Cell,
73:1155-1164 (1993); Araki et al., Proc. Natl. Acad. Sci. USA,
92:160-164 (1995); Lakso et al., Proc. Natl. Acad. Sci. USA,
89:6232-6236 (1992); and Orban et al., Proc. Natl. Acad. Sci. USA,
89:6861-6865 (1992).
[0270] The transgenic animals of the present invention may be
transgenic animals that carry a transgene in all cells or mosaic
transgenic animals carrying a transgene only in certain cells,
e.g., somatic cells. The transgenic animals may have a single copy
or multiple copies of a particular transgene.
[0271] The founder transgenic animals thus produced may be bred to
produce various offsprings. For example, they can be inbred,
outbred, and crossbred to establish homozygous lines, heterozygous
lines, and compound homozygous or heterozygous lines.
8. Pharmaceutical Compositions and Formulations
[0272] In another aspect of the present invention, pharmaceutical
compositions are also provided containing one or more of the
therapeutic agents provided in the present invention as described
in Section 6. The compositions are prepared as a pharmaceutical
formulation suitable for administration into a patient.
Accordingly, the present invention also extends to pharmaceutical
compositions, medicaments, drugs or other compositions containing
one or more of the therapeutic agent in accordance with the present
invention.
[0273] For example, such therapeutic agents include, but are not
limited to, (1) small organic compounds selected based on the
screening methods of the present invention capable of interfering
with the interaction between APOA1 and an interactor thereof, (2)
antisense compounds specifically hybridizable to APOA1 nucleic
acids (gene or mRNA) (3) antisense compounds specific to the gene
or mRNA of an APOA1 -interacting protein, (4) ribozyme compounds
specific to APOA1 nucleic acids (gene or mRNA), (5) ribozyme
compounds specific to the gene or mRNA of an APOA1-interacting
protein, (6) antibodies immunoreactive with APOA1 or an
APOA1-interacting protein, (7) antibodies selectively
immunoreactive with a protein complex of the present invention, (8)
small organic compounds capable of binding a protein complex of the
present invention, (9) small peptide compounds as described above
(optionally linked to a transporter) capable of interacting with
APOA1 or an APOA1-interacting protein, (10) nucleic acids encoding
the antibodies or peptides, etc.
[0274] The compositions are prepared as a pharmaceutical
formulation suitable for administration into a patient.
Accordingly, the present invention also extends to pharmaceutical
compositions, medicaments, drugs or other compositions containing
one or more of the therapeutic agent in accordance with the present
invention.
[0275] In the pharmaceutical composition, an active compound
identified in accordance with the present invention can be in any
pharmaceutically acceptable salt form. As used herein, the term
"pharmaceutically acceptable salts" refers to the relatively
non-toxic, organic or inorganic salts of the compounds of the
present invention, including inorganic or organic acid addition
salts of the compound. Examples of such salts include, but are not
limited to, hydrochloride salts, sulfate salts, bisulfate salts,
borate salts, nitrate salts, acetate salts, phosphate salts,
hydrobromide salts, laurylsulfonate salts, glucoheptonate salts,
oxalate salts, oleate salts, laurate salts, stearate salts,
palmitate salts, valerate salts, benzoate salts, naththylate salts,
mesylate salts, tosylate salts, citrate salts, lactate salts,
maleate salts, succinate salts, tartrate salts, fumarate salts, and
the like. See, e.g., Berge, et al., J. Pharm. Sci., 66:1-19
(1977).
[0276] For oral delivery, the active compounds can be incorporated
into a formulation that includes pharmaceutically acceptable
carriers such as binders (e.g., gelatin, cellulose, gum
tragacanth), excipients (e.g., starch, lactose), lubricants (e.g.,
magnesium stearate, silicon dioxide), disintegrating agents (e.g.,
alginate, Primogel, and corn starch), and sweetening or flavoring
agents (e.g., glucose, sucrose, saccharin, methyl salicylate, and
peppermint). The formulation can be orally delivered in the form of
enclosed gelatin capsules or compressed tablets. Capsules and
tablets can be prepared in any conventional techniques. The
capsules and tablets can also be coated with various coatings known
in the art to modify the flavors, tastes, colors, and shapes of the
capsules and tablets. In addition, liquid carriers such as fatty
oil can also be included in capsules.
[0277] Suitable oral formulations can also be in the form of
suspension, syrup, chewing gum, wafer, elixir, and the like. If
desired, conventional agents for modifying flavors, tastes, colors,
and shapes of the special forms can also be included. In addition,
for convenient administration by enteral feeding tube in patients
unable to swallow, the active compounds can be dissolved in an
acceptable lipophilic vegetable oil vehicle such as olive oil, corn
oil and safflower oil.
[0278] The active compounds can also be administered parenterally
in the form of solution or suspension, or in lyophilized form
capable of conversion into a solution or suspension form before
use. In such formulations, diluents or pharmaceutically acceptable
carriers such as sterile water and physiological saline buffer can
be used. Other conventional solvents, pH buffers, stabilizers,
anti-bacterial agents, surfactants, and antioxidants can all be
included. For example, useful components include sodium chloride,
acetate, citrate or phosphate buffers, glycerin, dextrose, fixed
oils, methyl parabens, polyethylene glycol, propylene glycol,
sodium bisulfate, benzyl alcohol, ascorbic acid, and the like. The
parenteral formulations can be stored in any conventional
containers such as vials and ampoules.
[0279] Routes of topical administration include nasal, bucal,
mucosal, rectal, or vaginal applications. For topical
administration, the active compounds can be formulated into
lotions, creams, ointments, gels, powders, pastes, sprays,
suspensions, drops and aerosols. Thus, one or more thickening
agents, humectants, and stabilizing agents can be included in the
formulations. Examples of such agents include, but are not limited
to, polyethylene glycol, sorbitol, xanthan gum, petrolatum,
beeswax, or mineral oil, lanolin, squalene, and the like. A special
form of topical administration is delivery by a transdermal patch.
Methods for preparing transdermal patches are disclosed, e.g., in
Brown, et al., Annual Review of Medicine, 39:221-229 (1988), which
is incorporated herein by reference.
[0280] Subcutaneous implantation for sustained release of the
active compounds may also be a suitable route of administration.
This entails surgical procedures for implanting an active compound
in any suitable formulation into a subcutaneous space, e.g.,
beneath the anterior abdominal wall. See, e.g., Wilson et al., J.
Clin. Psych. 45:242-247 (1984). Hydrogels can be used as a carrier
for the sustained release of the active compounds. Hydrogels are
generally known in the art. They are typically made by crosslinking
high molecular weight biocompatible polymers into a network that
swells in water to form a gel like material. Preferably, hydrogels
is biodegradable or biosorbable. For purposes of this invention,
hydrogels made of polyethylene glycols, collagen, or
poly(glycolic-.alpha.-L-lactic acid) may be useful. See, e.g.,
Phillips et al., J. Pharmaceut. Sci. 73:1718-1720 (1984).
[0281] The active compounds can also be conjugated, to a water
soluble non-immunogenic non-peptidic high molecular weight polymer
to form a polymer conjugate. For example, an active compound is
covalently linked to polyethylene glycol to form a conjugate.
Typically, such a conjugate exhibits improved solubility,
stability, and reduced toxicity and immunogenicity. Thus, when
administered to a patient, the active compound in the conjugate can
have a longer half-life in the body, and exhibit better efficacy.
See generally, Burnham, Am. J. Hosp. Pharm., 15:210-218 (1994).
PEGylated proteins are currently being used in protein replacement
therapies and for other therapeutic uses. For example, PEGylated
interferon (PEG-INTRON A.RTM.) is clinically used for treating
Hepatitis B. PEGylated adenosine deaminase (ADAGEN.RTM.) is being
used to treat severe combined immunodeficiency disease (SCIDS).
PEGylated L-asparaginase (ONCAPSPAR.RTM.) is being used to treat
acute lymphoblastic leukemia (ALL). It is preferred that the
covalent linkage between the polymer and the active compound and/or
the polymer itself is hydrolytically degradable under physiological
conditions. Such conjugates known as "prodrugs" can readily release
the active compound inside the body. Controlled release of an
active compound can also be achieved by incorporating the active
ingredient into microcapsules, nanocapsules, or hydrogels generally
known in the art.
[0282] Liposomes can also be used as carriers for the active
compounds of the present invention. Liposomes are micelles made of
various lipids such as cholesterol, phospholipids, fatty acids, and
derivatives thereof. Various modified lipids can also be used.
Liposomes can reduce the toxicity of the active compounds, and
increase their stability. Methods for preparing liposomal
suspensions containing active ingredients therein are generally
known in the art. See, e.g., U.S. Pat. No. 4,522,811; Prescott,
Ed., Methods in Cell Biology, Volume XIV, Academic Press, New York,
N.Y. (1976).
[0283] The active compounds can also be administered in combination
with another active agent that synergistically treats or prevents
the same symptoms or is effective for another disease or symptom in
the patient treated so long as the other active agent does not
interfere with or adversely affect the effects of the active
compounds of this invention. Such other active agents include but
are not limited to anti-inflammation agents, antiviral agents,
antibiotics, antifungal agents, antithrombotic agents,
cardiovascular drugs, cholesterol lowering agents, anti-cancer
drugs, hypertension drugs, and the like.
[0284] Generally, the toxicity profile and therapeutic efficacy of
the therapeutic agents can be determined by standard pharmaceutical
procedures in cell models or animal models, e.g., those provided in
Section 7. As is known in the art, the LD.sub.50 represents the
dose lethal to about 50% of a tested population. The ED.sub.50 is a
parameter indicating the dose therapeutically effective in about
50% of a tested population. Both LD.sub.50 and ED.sub.50 can be
determined in cell models and animal models. In addition, the
IC.sub.50 may also be obtained in cell models and animal models,
which stands for the circulating plasma concentration that is
effective in achieving about 50% of the maximal inhibition of the
symptoms of a disease or disorder. Such data may be used in
designing a dosage range for clinical trials in humans. Typically,
as will be apparent to skilled artisans, the dosage range for human
use should be designed such that the range centers around the
ED.sub.50 and/or IC.sub.50, but significantly below the LD.sub.50
obtained from cell or animal models.
[0285] It will be apparent to skilled artisans that therapeutically
effective amount for each active compound to be included in a
pharmaceutical composition of the present invention can vary with
factors including but not limited to the activity of the compound
used, stability of the active compound in the patient's body, the
severity of the conditions to be alleviated, the total weight of
the patient treated, the route of administration, the ease of
absorption, distribution, and excretion of the active compound by
the body, the age and sensitivity of the patient to be treated, and
the like. The amount of administration can also be adjusted as the
various factors change over time.
EXAMPLES
[0286] 1. Yeast Two-Hybrid System
[0287] The principles and methods of the yeast two-hybrid system
have been described in detail in The Yeast Two-Hybrid System,
Bartel and Fields, eds., pages 183-196, Oxford University Press,
New York, N.Y., 1997. The following is thus a description of the
particular procedure that we used, which was applied to all
proteins.
[0288] The cDNA encoding the bait protein was generated by PCR from
cDNA prepared from a desired tissue. The cDNA product was then
introduced by recombination into the yeast expression vector
pGBT.Q, which is a close derivative of pGBT.C (See Bartel et al.,
Nat Genet., 12:72-77 (1996)) in which the polylinker site has been
modified to include M13 sequencing sites. The new construct was
selected directly in the yeast strain PNY200 for its ability to
drive tryptophane synthesis (genotype of this strain: MAT.alpha.
trp1-901 leu2-3,112 ura3-52 his3-200 ade2 gal4.DELTA. gal80). In
these yeast cells, the bait was produced as a C-terminal fusion
protein with the DNA binding domain of the transcription factor
Gal4 (amino acids 1 to 147). Prey libraries were transformed into
the yeast strain BK100 (genotype of this strain: MAT.alpha.
trp1-901 leu2-3,112 ura3-52 his3-200 gal4.DELTA.gal80
LYS2::GAL-HIS3 GAL2-ADE2 met2::GAL7-lacZ), and selected for the
ability to drive leucine synthesis. In these yeast cells, each cDNA
was expressed as a fusion protein with the transcription activation
domain of the transcription factor Gal4 (amino acids 768 to 881)
and a 9 amino acid hemagglutinin epitope tag. PNY200 cells
(MAT.alpha. mating type), expressing the bait, were then mated with
BK100 cells (MAT.alpha. mating type), expressing prey proteins from
a prey library. The resulting diploid yeast cells expressing
proteins interacting with the bait protein were selected for the
ability to synthesize tryptophan, leucine, histidine, and adenine.
DNA was prepared from each clone, transformed by electroporation
into E. coli strain KC8 (Clontech KC8 electrocompetent cells,
Catalog No. C2023-1), and the cells were selected on
ampicillin-containing plates in the absence of either tryptophane
(selection for the bait plasmid) or leucine (selection for the
library plasmid). DNA for both plasmids was prepared and sequenced
by the dideoxynucleotide chain termination method. The identity of
the bait cDNA insert was confirmed and the cDNA insert from the
prey library plasmid was identified using the BLAST program to
search against public nucleotide and protein databases. Plasmids
from the prey library were then individually transformed into yeast
cells together with a plasmid driving the synthesis of lamin and 5
other test proteins, respectively, fused to the Gal4 DNA binding
domain. Clones that gave a positive signal in the
.beta.-galactosidase assay were considered false-positives and
discarded. Plasmids for the remaining clones were transformed into
yeast cells together with the original bait plasmid. Clones that
gave a positive signal in the .beta.-galactosidase assay were
considered true positives.
[0289] Bait sequences indicated in Table I were used in the yeast
two-hybrid system described above. The isolated prey sequences are
summarized in Table I. The GenBank Accession Nos. for the bait and
prey proteins are also provided in Table I, upon which the bait and
prey sequences are aligned.
[0290] 2. Production of Antibodies Selectively Immunoreactive with
Protein Complex
[0291] The APOA1-interacting region of PRA1 and the
PRA1-interacting region of APOA1 are indicated in Table I in
Section 2. Both regions, or fragments thereof, are
recombinantly-expressed in E. coli. and isolated and purified.
Mixing the two purified interacting regions forms a protein
complex. A protein complex is also formed by mixing recombinantly
expressed intact complete APOA1 and PRA1. The two protein complexes
are used as antigens in immunizing a mouse. mRNA is isolated from
the immunized mouse spleen cells, and first-strand cDNA is
synthesized using the mRNA as a template. The V.sub.H and V.sub.K
genes are amplified from the thus synthesized cDNAs by PCR using
appropriate primers.
[0292] The amplified V.sub.H and V.sub.K genes are ligated together
and subcloned into a phagemid vector for the construction of a
phage display library. E. coli. cells are transformed with the
ligation mixtures, and thus a phage display library is established.
Alternatively, the ligated V.sub.H and V.sub.k genes are subcloned
into a vector suitable for ribosome display in which the
V.sub.H-V.sub.k sequence is under the control of a T7 promoter. See
Schaffitzel et al., J. Immun. Meth., 231:119-135 (1999).
[0293] The libraries are screened for their ability to bind
APOA1-PRA1 complex and APOA1 or PRA1, alone. Several rounds of
screening are generally performed. Clones corresponding to scFv
fragments that bind the APOA1-PRA1 complex, but not isolated APOA1
or PRA1 are selected and purified. A single purified clone is used
to prepare an antibody selectively immunoreactive with the complex
comprising APOA1 and PRA1. The antibody is then verified by an
immunochemistry method such as RIA and ELISA.
[0294] In addition, the clones corresponding to scFv fragments that
bind the complex comprising APOA1 and PRA1, and also bind isolated
APOA1 and/or PRA1 may be selected. The scFv genes in the clones are
diversified by mutagenesis methods such as oligonucleotide-directed
mutagenesis, error-prone PCR (See Lin-Goerke et al., Biotechniques,
23:409 (1997)), dNTP analogues (See Zaccolo et al., J. Mol. Biol.,
255:589 (1996)), and other methods. The diversified clones are
further screened in phage display or ribosome display libraries. In
this manner, scFv fragments selectively immunoreactive with the
complex comprising APOA1 and PRA1 may be obtained.
[0295] 3. Yeast Screen to Identify Small Molecule Inhibitors of the
Interaction Between APOA1 and PRA1
[0296] Beta-galactosidase is used as a reporter enzyme to signal
the interaction between yeast two-hybrid protein pairs expressed
from plasmids in Saccharomyces cerevisiae. Yeast strain MY209 (ade2
his3 leu2 trp1 cyh2 ura3::GAL1p-lacZgal4 gal80 lys2::GAL1p-HIS3)
bearing one plasmid with the genotype of LEU2 CEN4 ARS1ADH1
p-SV40NLS-GAL4 (768-881)-PRA1-PGK1tAmpR ColE_ori, and another
plasmid having a genotype of TRP1 CEN4 ARS
ADH1p-GAL4(1-147)-APOA1-ADH1t AmpR ColE1_ori is cultured in
synthetic complete media lacking leucine and tryptophan (SC -Leu
-Trp) overnight at 30.degree. C. The APOA1 and PRA1 nucleic acids
in the plasmids can code for the full-length APOA1 and PRA1
proteins, respectively, or fragments thereof. This culture is
diluted to 0.01 OD.sub.630 units/ml using SC -Leu -Trp media. The
diluted MY209 culture is dispensed into 96-well microplates.
Compounds from a library of small molecules are added to the
microplates; the final concentration of test compounds is
approximately 60 .mu.M. The assay plates are incubated at
30.degree. C. overnight.
[0297] The following day an aliquot of concentrated substrate/lysis
buffer is added to each well and the plates incubated at 37.degree.
C. for 1-2 hours. At an appropriate time an aliquot of stop
solution is added to each well to halt the beta-galactosidase
reaction. For all microplates an absorbance reading is obtained to
assay the generation of product from the enzyme substrate. The
presence of putative inhibitors of the interaction between APOA1
and PRA1 results in inhibition of the beta-galactosidase signal
generated by MY209. Additional testing eliminates compounds that
decreased expression of beta-galactosidase by affecting yeast cell
growth and non-specific inhibitors that affected the
beta-galactosidase signal generated by the interaction of an
unrelated protein pair.
[0298] Once a hit, i.e., a compound which inhibits the interaction
between the interacting proteins, is obtained, the compound is
identified and subjected to further testing wherein the compounds
are assayed at several concentrations to determine an IC.sub.50
value, this being the concentration of the compound at which the
signal seen in the two-hybrid assay described in this Example is
50% of the signal seen in the absence of the inhibitor.
[0299] 4. Enzyme-Linked Immunosorbent Assay (ELISA)
[0300] pGEX5X-2 (Amersham Biosciences; Uppsala, Sweden) is used for
the expression of a GST-PRA1 fusion protein. The pGEX5X-2-PRA1
construct is transfected into Escherichia coli strain DH5.alpha.
(Invitrogen; Carlsbad, Calif.) and fusion protein is prepared by
inducing log phase cells (O.D. 595=0.4) with 0.2 mM
isopropyl-.beta.-D-thiogalactopyranoside (IPTG). Cultures are
harvested after approximately 4 hours of induction, and cells
pelleted by centrifugation. Cell pellets are resuspended in lysis
buffer (1% nonidet P-40 [NP-40], 150 mM NaCl, 10 mM Tris pH 7.4, 1
mM ABESF [4-(2-aminoethyl) benzenesulfonyl fluoride]), lysed by
sonication and the lysate cleared of insoluble materials by
centrifugation. Cleared lysate is incubated with Glutathione
Sepharose beads (Amersham Biosciences; Uppsala, Sweden) followed by
thorough washing with lysis buffer. The GST-PRA1 fusion protein is
then eluted from the beads with 5 mM reduced glutathione. Eluted
protein is dialyzed against phosphate buffer saline (PBS) to remove
the reduced glutathione.
[0301] A stable Drosophila Schneider 2 (S2) myc-APOA1 expression
cell line is generated by transfecting S2 cells with pCoHygro
(Invitrogen; Carlsbad, Calif.) and an expression vector that
directs the expression of the myc-APOA1 fusion protein. Briefly, S2
cells are washed and re-suspended in serum free Express Five media
(Invitrogen; Carlsbad, Calif.). Plasmid/liposome complexes are then
added (NovaFECTOR, Venn Nova; Pompano Beach, Fla.) and allowed to
incubate with cells for 12 hours under standard growth conditions
(room temperature, no CO.sub.2 buffering). Following this
incubation period fetal bovine serum is added to a final
concentration of 20% and cells are allowed to recover for 24 hours.
The media is replaced and cells are grown for an additional 24
hours. Transfected cells are then selected in 350 .mu.g/ml
hygromycin for three weeks. Expression of myc-APOA1 is confirmed by
Western blotting. This cell line is referred to as
S2-myc-APOA1.
[0302] GST-PRA1 fusion protein is immobilized to wells of an ELISA
plate as follows: Nunc Maxisorb 96 well ELISA plates (Nalge Nunc
International; Rochester, N.Y.) are incubated with 100 .mu.l of 10
.mu.g/ml of GST-PRA1 in 50 mM carbonate buffer (pH 9.6) and stored
overnight at 4.degree. Celsius. This plate is referred to as the
ELISA plate.
[0303] A compound dilution plate is generated in the following
manner. In a 96 well polypropylene plate (Greiner, Germany) 50
.mu.l of DMSO is pipetted into columns 2-12. In the same
polypropylene plate pipette, 10 .mu.l of each compound being tested
for its ability to modulate protein-protein interactions is plated
in the wells of column 1 followed by 90 .mu.l of DMSO (final volume
of 100 .mu.l). Compounds selected from primary screens or from
virtual screening, or designed based on the primary screen hits are
then serially diluted by removing 50 .mu.l from column 1 and
transferring it to column 2 (50:50 dilution). Serial dilutions are
continued until column 10. This plate is termed the compound
dilution plate.
[0304] Next, 12 .mu.l from each well of the compound dilution plate
is transferred into its corresponding well in a new polypropylene
plate. 108 .mu.l of S2-myc-APOA1-containing lysate
(1.times.10.sup.6 cell equivalents/ml) in phosphate buffered saline
is added to all wells of columns 1-11. 108 .mu.l of phosphate
buffered saline without lysate is added into all wells of column
12. The plate is then mixed on a shaker for 15 minutes. This plate
is referred to as the compound preincubation plate.
[0305] The ELISA plate is emptied of its contents and 400 .mu.l of
Superblock (Pierce Endogen; Rockford, Ill.) is added to all the
wells and allowed to sit for 1 hour at room temperature. 100 .mu.l
from all columns of the compound preincubation plate are
transferred into the corresponding wells of the ELISA binding
plate. The plate is then covered and allowed to incubate for 1.5
hours room temperature.
[0306] The interaction of the myc-tagged APOA1 with the immobilized
GST-PRA1 is detected by washing the ELISA plate followed by an
incubation with 100 .mu./well of 1 .mu.g/ml of mouse anti-myc IgG
(clone 9E10; Roche Applied Science; Indianapolis, Ind.) in
phosphate buffered saline. After 1 hour at room temperature, the
plates are washed with phosphate buffered saline and incubated with
100 .mu.l/well of 250 ng/ml of goat anti-mouse IgG conjugated to
horseradish peroxidase in phosphate buffer saline. Plates are then
washed again with phosphate buffered saline and incubated with the
fluorescent substrate solution Quantiblu (Pierce Endogen; Rockford,
Ill.). Horseradish peroxidase activity is then measured by reading
the plates in a fluorescent plate reader (325 nm excitation, 420 nm
emission).
[0307] Although the foregoing invention has been described in some
detail by way of illustration and example for purposes of clarity
of understanding, it will be obvious that certain changes and
modifications may be practiced within the scope of the appended
claims.
[0308] In various parts of this disclosure, certain publications or
patents are discussed or cited. The mere discussion of, or
reference to, such publications or patents is not intended as
admission that they are prior art to the present invention.
* * * * *
References